From cdada851015ce30a858aec2082b7a6dbaf9aca87 Mon Sep 17 00:00:00 2001 From: samuel-marsh Date: Mon, 13 Sep 2021 14:38:34 -0400 Subject: [PATCH 01/53] add violin raster --- DESCRIPTION | 1 + R/visualization.R | 46 +++++++++++++++++++++++++++++++++++----------- 2 files changed, 36 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2c56f1980..ec840ef4f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -34,6 +34,7 @@ Imports: future, future.apply, ggplot2 (>= 3.3.0), + ggrastr, ggrepel, ggridges, graphics, diff --git a/R/visualization.R b/R/visualization.R index 25d74c015..1f98854ef 100644 --- a/R/visualization.R +++ b/R/visualization.R @@ -554,6 +554,8 @@ RidgePlot <- function( #' single violin shapes. #' @param adjust Adjust parameter for geom_violin #' @param flip flip plot orientation (identities on x-axis) +#' @param raster Convert points to raster format, default is \code{NULL} which +#' automatically rasterizes if plotting more than 100,000 cells #' #' @return A \code{\link[patchwork]{patchwork}ed} ggplot object if #' \code{combine = TRUE}; otherwise, a list of ggplot objects @@ -588,7 +590,8 @@ VlnPlot <- function( stack = FALSE, combine = TRUE, fill.by = 'feature', - flip = FALSE + flip = FALSE, + raster = NULL ) { if ( !is.null(x = split.by) & @@ -623,7 +626,8 @@ VlnPlot <- function( stack = stack, combine = combine, fill.by = fill.by, - flip = flip + flip = flip, + raster = raster )) } @@ -5543,6 +5547,8 @@ DefaultDimReduc <- function(object, assay = NULL) { # ggplot object. If \code{FALSE}, return a list of ggplot objects # @param fill.by Color violins/ridges based on either 'feature' or 'ident' # @param flip flip plot orientation (identities on x-axis) +# @param raster Convert points to raster format, default is \code{NULL} which +# automatically rasterizes if plotting more than 100,000 cells # # @return A \code{\link[patchwork]{patchwork}ed} ggplot object if # \code{combine = TRUE}; otherwise, a list of ggplot objects @@ -5571,7 +5577,8 @@ ExIPlot <- function( stack = FALSE, combine = TRUE, fill.by = NULL, - flip = FALSE + flip = FALSE, + raster = NULL ) { assay <- assay %||% DefaultAssay(object = object) DefaultAssay(object = object) <- assay @@ -5672,7 +5679,8 @@ ExIPlot <- function( adjust = adjust, cols = cols, pt.size = pt.size, - log = log + log = log, + raster = raster )) } ) @@ -7183,6 +7191,8 @@ SingleDimPlot <- function( # @param cols Colors to use for plotting # @param log plot Y axis on log scale # @param seed.use Random seed to use. If NULL, don't set a seed +# @param raster Convert points to raster format, default is \code{NULL} which +# automatically rasterizes if plotting more than 100,000 cells # # @return A ggplot-based Expression-by-Identity plot # @@ -7191,6 +7201,7 @@ SingleDimPlot <- function( #' @importFrom utils globalVariables #' @importFrom ggridges geom_density_ridges theme_ridges #' @importFrom ggplot2 ggplot aes_string theme labs geom_violin geom_jitter ylim position_jitterdodge +#' @importFrom ggrastr rasterize #' scale_fill_manual scale_y_log10 scale_x_log10 scale_y_discrete scale_x_continuous waiver #' @importFrom cowplot theme_cowplot #' @@ -7205,7 +7216,8 @@ SingleExIPlot <- function( pt.size = 0, cols = NULL, seed.use = 42, - log = FALSE + log = FALSE, + raster = NULL ) { if (!is.null(x = seed.use)) { set.seed(seed = seed.use) @@ -7266,13 +7278,25 @@ SingleExIPlot <- function( theme(axis.text.x = element_text(angle = 45, hjust = 1)) ) if (is.null(x = split)) { - jitter <- geom_jitter(height = 0, size = pt.size, show.legend = FALSE) + if (isTRUE(x = raster)) { + jitter <- rasterize(geom_jitter(height = 0, size = pt.size, show.legend = FALSE)) + } else { + jitter <- geom_jitter(height = 0, size = pt.size, show.legend = FALSE) + } } else { - jitter <- geom_jitter( - position = position_jitterdodge(jitter.width = 0.4, dodge.width = 0.9), - size = pt.size, - show.legend = FALSE - ) + if (isTRUE(x = raster)) { + jitter <- rasterize(geom_jitter( + position = position_jitterdodge(jitter.width = 0.4, dodge.width = 0.9), + size = pt.size, + show.legend = FALSE + )) + } else { + jitter <- geom_jitter( + position = position_jitterdodge(jitter.width = 0.4, dodge.width = 0.9), + size = pt.size, + show.legend = FALSE + ) + } } log.scale <- scale_y_log10() axis.scale <- ylim From 25725fcf76dcda6f65fe77882c1d4dbbdc882400 Mon Sep 17 00:00:00 2001 From: samuel-marsh Date: Tue, 14 Sep 2021 06:55:16 -0400 Subject: [PATCH 02/53] add number of points check --- R/visualization.R | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/R/visualization.R b/R/visualization.R index 1f98854ef..10a8ad7c5 100644 --- a/R/visualization.R +++ b/R/visualization.R @@ -7219,6 +7219,13 @@ SingleExIPlot <- function( log = FALSE, raster = NULL ) { + if ((nrow(x = data) > 1e5) & !isFALSE(raster)){ + message("Rasterizing points since number of points exceeds 100,000.", + "\nTo disable this behavior set `raster=FALSE`") + } + raster <- raster %||% (nrow(x = data) > 1e5) + + if (!is.null(x = seed.use)) { set.seed(seed = seed.use) } From 58fcb405b5bb0f7c801ef18770c3c88037cc5f27 Mon Sep 17 00:00:00 2001 From: Yaman Qalieh Date: Tue, 14 Sep 2021 01:35:46 -0400 Subject: [PATCH 03/53] Skip groups with fewer than default min.cells.group (Fixes #1971) --- R/differential_expression.R | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/R/differential_expression.R b/R/differential_expression.R index a579d36ef..b4134fa14 100644 --- a/R/differential_expression.R +++ b/R/differential_expression.R @@ -241,6 +241,7 @@ FindConservedMarkers <- function( grouping.var, assay = 'RNA', slot = 'data', + min.cells.group = 3, meta.method = metap::minimump, verbose = TRUE, ... @@ -298,6 +299,20 @@ FindConservedMarkers <- function( } ident.2 <- ident.2.save cells.1 <- WhichCells(object = object, idents = ident.use.1) + if (length(cells.1) < min.cells.group) { + warning( + level.use, + " has fewer than ", + min.cells.group, + " cells in Identity: ", + paste(ident.1, collapse = ", "), + ". Skipping ", + level.use, + call. = FALSE, + immediate. = TRUE + ) + next + } if (is.null(x = ident.2)) { cells.2 <- setdiff(x = cells[[i]], y = cells.1) ident.use.2 <- names(x = which(x = table(Idents(object = object)[cells.2]) > 0)) From 38c6b243da5f113ebb0b33f4b9dceb9f9141696e Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Tue, 14 Sep 2021 13:33:04 -0400 Subject: [PATCH 04/53] Export utility funcitons --- DESCRIPTION | 1 + NAMESPACE | 13 ++ R/utilities.R | 56 ++--- R/visualization.R | 433 +++++++++++++++++++-------------------- man/AutoPointSize.Rd | 24 +++ man/DimHeatmap.Rd | 2 +- man/PercentAbove.Rd | 24 +++ man/SetQuantile.Rd | 27 +++ man/SingleCorPlot.Rd | 52 +++++ man/SingleDimPlot.Rd | 80 ++++++++ man/SingleExIPlot.Rd | 51 +++++ man/SingleImageMap.Rd | 22 ++ man/SingleRasterMap.Rd | 44 ++++ man/SingleSpatialPlot.Rd | 72 +++++++ 14 files changed, 644 insertions(+), 257 deletions(-) create mode 100644 man/AutoPointSize.Rd create mode 100644 man/PercentAbove.Rd create mode 100644 man/SetQuantile.Rd create mode 100644 man/SingleCorPlot.Rd create mode 100644 man/SingleDimPlot.Rd create mode 100644 man/SingleExIPlot.Rd create mode 100644 man/SingleImageMap.Rd create mode 100644 man/SingleRasterMap.Rd create mode 100644 man/SingleSpatialPlot.Rd diff --git a/DESCRIPTION b/DESCRIPTION index ebdfc2352..6a8d01726 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -24,6 +24,7 @@ Authors@R: c( ) URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat BugReports: https://github.com/satijalab/seurat/issues +Remotes: mojaveazure/seurat-object@feat/standard Depends: R (>= 4.0.0), methods diff --git a/NAMESPACE b/NAMESPACE index c847f2c78..4e5c87530 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -124,6 +124,7 @@ export(AggregateExpression) export(AnnotateAnchors) export(Assays) export(AugmentPlot) +export(AutoPointSize) export(AverageExpression) export(BGTextColor) export(BarcodeInflectionsPlot) @@ -247,6 +248,7 @@ export(NormalizeData) export(PCAPlot) export(PCASigGenes) export(PCHeatmap) +export(PercentAbove) export(PercentageFeatureSet) export(PlotClusterTree) export(PlotPerturbScore) @@ -299,8 +301,15 @@ export(SelectIntegrationFeatures) export(SetAssayData) export(SetIdent) export(SetIntegrationData) +export(SetQuantile) export(SeuratAxes) export(SeuratTheme) +export(SingleCorPlot) +export(SingleDimPlot) +export(SingleExIPlot) +export(SingleImageMap) +export(SingleRasterMap) +export(SingleSpatialPlot) export(SpatialDimPlot) export(SpatialFeaturePlot) export(SpatialPlot) @@ -399,6 +408,7 @@ importFrom(SeuratObject,CreateAssayObject) importFrom(SeuratObject,CreateDimReducObject) importFrom(SeuratObject,CreateSeuratObject) importFrom(SeuratObject,DefaultAssay) +importFrom(SeuratObject,DefaultDimReduc) importFrom(SeuratObject,Distances) importFrom(SeuratObject,Embeddings) importFrom(SeuratObject,FetchData) @@ -417,6 +427,7 @@ importFrom(SeuratObject,Loadings) importFrom(SeuratObject,LogSeuratCommand) importFrom(SeuratObject,Misc) importFrom(SeuratObject,Neighbors) +importFrom(SeuratObject,PackageCheck) importFrom(SeuratObject,Project) importFrom(SeuratObject,Radius) importFrom(SeuratObject,Reductions) @@ -545,11 +556,13 @@ importFrom(grDevices,col2rgb) importFrom(grDevices,colorRampPalette) importFrom(grDevices,rgb) importFrom(graphics,axis) +importFrom(graphics,image) importFrom(graphics,locator) importFrom(graphics,par) importFrom(graphics,plot) importFrom(graphics,plot.new) importFrom(graphics,smoothScatter) +importFrom(graphics,title) importFrom(grid,addGrob) importFrom(grid,editGrob) importFrom(grid,gTree) diff --git a/R/utilities.R b/R/utilities.R index 6ae270517..c5710b6be 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -1,4 +1,5 @@ #' @include generics.R +#' @importFrom SeuratObject PackageCheck #' NULL @@ -1081,6 +1082,25 @@ MinMax <- function(data, min, max) { return(data2) } +#' Calculate the percentage of a vector above some threshold +#' +#' @param x Vector of values +#' @param threshold Threshold to use when calculating percentage +#' +#' @return Returns the percentage of \code{x} values above the given threshold +#' +#' @export +#' +#' @export +#' +#' @examples +#' set.seed(42) +#' PercentAbove(sample(1:100, 10), 75) +#' +PercentAbove <- function(x, threshold) { + return(length(x = x[x > threshold]) / length(x = x)) +} + #' Calculate the percentage of all counts that belong to a given set of features #' #' This function enables you to easily calculate the percentage of all the counts belonging to a @@ -2158,31 +2178,6 @@ Online <- function(url, strict = FALSE, seconds = 5L) { return(comp(x = status_code(x = request), y = code)) } -# Check the existence of a package -# -# @param ... Package names -# @param error If true, throw an error if the package doesn't exist -# -# @return Invisibly returns boolean denoting if the package is installed -# -PackageCheck <- function(..., error = TRUE) { - pkgs <- unlist(x = c(...), use.names = FALSE) - package.installed <- vapply( - X = pkgs, - FUN = requireNamespace, - FUN.VALUE = logical(length = 1L), - quietly = TRUE - ) - if (error && any(!package.installed)) { - stop( - "Cannot find the following packages: ", - paste(pkgs[!package.installed], collapse = ', '), - ". Please install" - ) - } - invisible(x = package.installed) -} - # Parenting parameters from one environment to the next # # This function allows one to modify a parameter in a parent environment @@ -2231,17 +2226,6 @@ Parenting <- function(parent.find = 'Seurat', ...) { } } -# Calculate the percentage of a vector above some threshold -# -# @param x Vector of values -# @param threshold Threshold to use when calculating percentage -# -# @return Returns the percentage of `x` values above the given threshold -# -PercentAbove <- function(x, threshold) { - return(length(x = x[x > threshold]) / length(x = x)) -} - # Generate a random name # # Make a name from randomly sampled lowercase letters, diff --git a/R/visualization.R b/R/visualization.R index a06d64798..60ea3e225 100644 --- a/R/visualization.R +++ b/R/visualization.R @@ -1,5 +1,6 @@ #' @importFrom utils globalVariables #' @importFrom ggplot2 ggproto GeomViolin +#' @importFrom SeuratObject DefaultDimReduc #' NULL @@ -16,7 +17,7 @@ NULL #' @param dims Dimensions to plot #' @param nfeatures Number of genes to plot #' @param cells A list of cells to plot. If numeric, just plots the top cells. -#' @param reduction Which dimmensional reduction to use +#' @param reduction Which dimensional reduction to use #' @param balanced Plot an equal number of genes with both + and - scores. #' @param projected Use the full projected dimensional reduction #' @param ncol Number of columns to plot @@ -3995,6 +3996,29 @@ AugmentPlot <- function(plot, width = 10, height = 10, dpi = 100) { return(blank) } +#' Automagically calculate a point size for ggplot2-based scatter plots +#' +#' It happens to look good +#' +#' @param data A data frame being passed to ggplot2 +#' @param raster If TRUE, point size is set to 1 +#' +#' @return The "optimal" point size for visualizing these data +#' +#' @export +#' +#' @examples +#' df <- data.frame(x = rnorm(n = 10000), y = runif(n = 10000)) +#' AutoPointSize(data = df) +#' +AutoPointSize <- function(data, raster = NULL) { + return(ifelse( + test = isTRUE(x = raster), + yes = 1, + no = min(1583 / nrow(x = data), 1) + )) +} + #' Determine text color based on background color #' #' @param background A vector of background colors; supports R color names and @@ -4909,6 +4933,40 @@ PurpleAndYellow <- function(k = 50) { return(CustomPalette(low = "magenta", high = "yellow", mid = "black", k = k)) } +#' Find the Quantile of Data +#' +#' Converts a quantile in character form to a number regarding some data. +#' String form for a quantile is represented as a number prefixed with +#' \dQuote{q}; for example, 10th quantile is \dQuote{q10} while 2nd quantile is +#' \dQuote{q2}. Will only take a quantile of non-zero data values +#' +#' @param cutoff The cutoff to turn into a quantile +#' @param data The data to turn find the quantile of +#' +#' @return The numerical representation of the quantile +#' +#' @importFrom stats quantile +#' +#' @export +#' +#' @examples +#' set.seed(42) +#' SetQuantile('q10', sample(1:100, 10)) +#' +SetQuantile <- function(cutoff, data) { + if (grepl(pattern = '^q[0-9]{1,2}$', x = as.character(x = cutoff), perl = TRUE)) { + this.quantile <- as.numeric(x = sub( + pattern = 'q', + replacement = '', + x = as.character(x = cutoff) + )) / 100 + data <- unlist(x = data) + data <- data[data > 0] + cutoff <- quantile(x = data, probs = this.quantile) + } + return(as.numeric(x = cutoff)) +} + #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% # Seurat themes #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% @@ -5259,27 +5317,6 @@ WhiteBackground <- function(...) { # Internal #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -# Automagically calculate a point size for ggplot2-based scatter plots -# -# It happens to look good -# -# @param data A data frame being passed to ggplot2 -# @param raster If TRUE, point size is set to 1 -# -# @return The "optimal" point size for visualizing these data -# -# @examples -# df <- data.frame(x = rnorm(n = 10000), y = runif(n = 10000)) -# AutoPointSize(data = df) -# -AutoPointSize <- function(data, raster = NULL) { - return(ifelse( - test = isTRUE(x = raster), - yes = 1, - no = min(1583 / nrow(x = data), 1) - )) -} - # Calculate bandwidth for use in ggplot2-based smooth scatter plots # # Inspired by MASS::bandwidth.nrd and graphics:::.smoothScatterCalcDensity @@ -5492,60 +5529,6 @@ Col2Hex <- function(...) { return(colors) } -# Find the default DimReduc -# -# Searches for DimReducs matching 'umap', 'tsne', or 'pca', case-insensitive, and -# in that order. Priority given to DimReducs matching the DefaultAssay or assay specified -# (eg. 'pca' for the default assay weights higher than 'umap' for a non-default assay) -# -# @param object A Seurat object -# @param assay Name of assay to use; defaults to the default assay of the object -# -# @return The default DimReduc, if possible -# -DefaultDimReduc <- function(object, assay = NULL) { - object <- UpdateSlots(object = object) - assay <- assay %||% DefaultAssay(object = object) - drs.use <- c('umap', 'tsne', 'pca') - dim.reducs <- FilterObjects(object = object, classes.keep = 'DimReduc') - drs.assay <- Filter( - f = function(x) { - return(DefaultAssay(object = object[[x]]) == assay) - }, - x = dim.reducs - ) - if (length(x = drs.assay) > 0) { - index <- lapply( - X = drs.use, - FUN = grep, - x = drs.assay, - ignore.case = TRUE - ) - index <- Filter(f = length, x = index) - if (length(x = index) > 0) { - return(drs.assay[min(index[[1]])]) - } - } - index <- lapply( - X = drs.use, - FUN = grep, - x = dim.reducs, - ignore.case = TRUE - ) - index <- Filter(f = length, x = index) - if (length(x = index) < 1) { - stop( - "Unable to find a DimReduc matching one of '", - paste(drs.use[1:(length(x = drs.use) - 1)], collapse = "', '"), - "', or '", - drs.use[length(x = drs.use)], - "', please specify a dimensional reduction to use", - call. = FALSE - ) - } - return(dim.reducs[min(index[[1]])]) -} - # Plot feature expression by identity # # Basically combines the codebase for VlnPlot and RidgePlot @@ -6798,35 +6781,6 @@ SetHighlight <- function( )) } -# Find the quantile of a data -# -# Converts a quantile in character form to a number regarding some data -# String form for a quantile is represented as a number prefixed with 'q' -# For example, 10th quantile is 'q10' while 2nd quantile is 'q2' -# -# Will only take a quantile of non-zero data values -# -# @param cutoff The cutoff to turn into a quantile -# @param data The data to turn find the quantile of -# -# @return The numerical representation of the quantile -# -#' @importFrom stats quantile -# -SetQuantile <- function(cutoff, data) { - if (grepl(pattern = '^q[0-9]{1,2}$', x = as.character(x = cutoff), perl = TRUE)) { - this.quantile <- as.numeric(x = sub( - pattern = 'q', - replacement = '', - x = as.character(x = cutoff) - )) / 100 - data <- unlist(x = data) - data <- data[data > 0] - cutoff <- quantile(x = data, probs = this.quantile) - } - return(as.numeric(x = cutoff)) -} - #' @importFrom shiny brushedPoints # ShinyBrush <- function(plot.data, brush, outputs, inverts = character(length = 0L)) {#}, selected = NULL) { @@ -6845,30 +6799,35 @@ ShinyBrush <- function(plot.data, brush, outputs, inverts = character(length = 0 } globalVariables(names = '..density..', package = 'Seurat') -# A single correlation plot -# -# @param data.plot A data frame with two columns to be plotted -# @param col.by A vector or factor of values to color the plot by -# @param cols An optional vector of colors to use -# @param pt.size Point size for the plot -# @param smooth Make a smoothed scatter plot -# @param rows.highight A vector of rows to highlight (like cells.highlight in SingleDimPlot) -# @param legend.title Optional legend title -# @param raster Convert points to raster format, default is \code{NULL} -# which will automatically use raster if the number of points plotted is greater than -# 100,000 -# @param jitter Jitter for easier visualization of crowded points -# -# @param ... Extra parameters to MASS::kde2d -# +#' A single correlation plot +#' +#' @param data A data frame with two columns to be plotted +#' @param col.by A vector or factor of values to color the plot by +#' @param cols An optional vector of colors to use +#' @param pt.size Point size for the plot +#' @param smooth Make a smoothed scatter plot +#' @param rows.highight A vector of rows to highlight (like cells.highlight in +#' \code{\link{SingleDimPlot}}) +#' @param legend.title Optional legend title +#' @param raster Convert points to raster format, default is \code{NULL} +#' which will automatically use raster if the number of points plotted is +#' greater than 100,000 +#' @param plot.cor ... +#' @param jitter Jitter for easier visualization of crowded points +#' +#' @return A ggplot2 object +#' #' @importFrom stats cor -# #' @importFrom MASS kde2d #' @importFrom cowplot theme_cowplot #' @importFrom RColorBrewer brewer.pal.info #' @importFrom ggplot2 ggplot aes_string geom_point labs scale_color_brewer #' scale_color_manual guides stat_density2d aes scale_fill_continuous #' @importFrom scattermore geom_scattermore #' +#' @keywords internal +#' +#' @export +#' SingleCorPlot <- function( data, col.by = NULL, @@ -7022,44 +6981,51 @@ SingleCorPlot <- function( return(plot) } -# Plot a single dimension -# -# @param data Data to plot -# @param dims A two-length numeric vector with dimensions to use -# @param pt.size Adjust point size for plotting -# @param col.by ... -# @param cols Vector of colors, each color corresponds to an identity class. This may also be a single character -# or numeric value corresponding to a palette as specified by \code{\link[RColorBrewer]{brewer.pal.info}}. -# By default, ggplot2 assigns colors -# @param shape.by If NULL, all points are circles (default). You can specify any cell attribute -# (that can be pulled with FetchData) allowing for both different colors and different shapes on -# cells. -# @param alpha.by Mapping variable for the point alpha value -# @param order Specify the order of plotting for the idents. This can be useful for crowded plots if -# points of interest are being buried. Provide either a full list of valid idents or a subset to be -# plotted last (on top). -# @param label Whether to label the clusters -# @param repel Repel labels -# @param label.size Sets size of labels -# @param cells.highlight A list of character or numeric vectors of cells to -# highlight. If only one group of cells desired, can simply -# pass a vector instead of a list. If set, colors selected cells to the color(s) -# in \code{cols.highlight} and other cells black (white if dark.theme = TRUE); -# will also resize to the size(s) passed to \code{sizes.highlight} -# @param cols.highlight A vector of colors to highlight the cells as; will -# repeat to the length groups in cells.highlight -# @param sizes.highlight Size of highlighted cells; will repeat to the length -# groups in cells.highlight -# @param na.value Color value for NA points when using custom scale. -# @param raster Convert points to raster format, default is \code{NULL} -# which will automatically use raster if the number of points plotted is greater than -# 100,000 -# +#' Plot a single dimension +#' +#' @param data Data to plot +#' @param dims A two-length numeric vector with dimensions to use +#' @param col.by ... +#' @param cols Vector of colors, each color corresponds to an identity class. +#' This may also be a single character or numeric value corresponding to a +#' palette as specified by \code{\link[RColorBrewer]{brewer.pal.info}}.By +#' default, ggplot2 assigns colors +#' @param pt.size Adjust point size for plotting +#' @param shape.by If NULL, all points are circles (default). You can specify +#' any cell attribute (that can be pulled with \code{\link{FetchData}}) +#' allowing for both different colors and different shapes on cells. +#' @param alpha.by Mapping variable for the point alpha value +#' @param order Specify the order of plotting for the idents. This can be +#' useful for crowded plots if points of interest are being buried. Provide +#' either a full list of valid idents or a subset to be plotted last (on top). +#' @param label Whether to label the clusters +#' @param repel Repel labels +#' @param label.size Sets size of labels +#' @param cells.highlight A list of character or numeric vectors of cells to +#' highlight. If only one group of cells desired, can simply +#' pass a vector instead of a list. If set, colors selected cells to the color(s) +#' in \code{cols.highlight} and other cells black (white if dark.theme = TRUE); +#' will also resize to the size(s) passed to \code{sizes.highlight} +#' @param cols.highlight A vector of colors to highlight the cells as; will +#' repeat to the length groups in cells.highlight +#' @param sizes.highlight Size of highlighted cells; will repeat to the length +#' groups in cells.highlight +#' @param na.value Color value for NA points when using custom scale. +#' @param raster Convert points to raster format, default is \code{NULL} +#' which will automatically use raster if the number of points plotted is +#' greater than 100,000 +#' +#' @return A ggplot2 object +#' #' @importFrom cowplot theme_cowplot #' @importFrom RColorBrewer brewer.pal.info #' @importFrom ggplot2 ggplot aes_string geom_point labs guides scale_color_brewer #' scale_color_manual element_rect guide_legend discrete_scale #' +#' @keywords internal +#' +#' @export +#' SingleDimPlot <- function( data, dims, @@ -7208,29 +7174,34 @@ SingleDimPlot <- function( return(plot) } -# Plot a single expression by identity on a plot -# -# @param type Make either a 'ridge' or 'violin' plot -# @param data Data to plot -# @param idents Idents to use -# @param sort Sort identity classes (on the x-axis) by the average -# expression of the attribute being potted -# @param y.max Maximum Y value to plot -# @param adjust Adjust parameter for geom_violin -# @param cols Colors to use for plotting -# @param log plot Y axis on log scale -# @param seed.use Random seed to use. If NULL, don't set a seed -# -# @return A ggplot-based Expression-by-Identity plot -# -# @import ggplot2 +#' Plot a single expression by identity on a plot +#' +#' @param data Data to plot +#' @param idents Idents to use +#' @param split Use a split violin plot +#' @param type Make either a \dQuote{ridge} or \dQuote{violin} plot +#' @param sort Sort identity classes (on the x-axis) by the average +#' expression of the attribute being potted +#' @param y.max Maximum Y value to plot +#' @param adjust Adjust parameter for geom_violin +#' @param pt.size Size of points for violin plots +#' @param cols Colors to use for plotting +#' @param seed.use Random seed to use. If NULL, don't set a seed +#' @param log plot Y axis on log scale +#' +#' @return A ggplot-based Expression-by-Identity plot +#' #' @importFrom stats rnorm #' @importFrom utils globalVariables #' @importFrom ggridges geom_density_ridges theme_ridges -#' @importFrom ggplot2 ggplot aes_string theme labs geom_violin geom_jitter ylim position_jitterdodge -#' scale_fill_manual scale_y_log10 scale_x_log10 scale_y_discrete scale_x_continuous waiver +#' @importFrom ggplot2 ggplot aes_string theme labs geom_violin geom_jitter +#' ylim position_jitterdodge scale_fill_manual scale_y_log10 scale_x_log10 +#' scale_y_discrete scale_x_continuous waiver #' @importFrom cowplot theme_cowplot #' +#' @keywords internal +#' @export +#' SingleExIPlot <- function( data, idents, @@ -7384,14 +7355,20 @@ SingleExIPlot <- function( return(plot) } -# A single heatmap from base R using image -# -# @param data matrix of data to plot -# @param order optional vector of cell names to specify order in plot -# @param title Title for plot -# -#' @importFrom graphics par plot.new -# +#' A single heatmap from base R using \code{\link[graphics]{image}} +#' +#' @param data matrix of data to plot +#' @param order optional vector of cell names to specify order in plot +#' @param title Title for plot +#' +#' @return No return, generates a base-R heatmap using \code{\link[graphics]{image}} +#' +#' @importFrom graphics axis image par plot.new title +#' +#' @keywords internal +#' +#' @export +#' SingleImageMap <- function(data, order = NULL, title = NULL) { if (!is.null(x = order)) { data <- data[order, ] @@ -7437,20 +7414,27 @@ SinglePolyPlot <- function(data, group.by, ...) { return(plot) } -# A single heatmap from ggplot2 using geom_raster -# -# @param data A matrix or data frame with data to plot -# @param raster switch between geom_raster and geom_tile -# @param cell.order ... -# @param feature.order ... -# @param cols A vector of colors to use -# @param disp.min Minimum display value (all values below are clipped) -# @param disp.max Maximum display value (all values above are clipped) -# @param limits A two-length numeric vector with the limits for colors on the plot -# @param group.by A vector to group cells by, should be one grouping identity per cell +#' A single heatmap from ggplot2 using geom_raster +#' +#' @param data A matrix or data frame with data to plot +#' @param raster switch between geom_raster and geom_tile +#' @param cell.order ... +#' @param feature.order ... +#' @param colors A vector of colors to use +#' @param disp.min Minimum display value (all values below are clipped) +#' @param disp.max Maximum display value (all values above are clipped) +#' @param limits A two-length numeric vector with the limits for colors on the plot +#' @param group.by A vector to group cells by, should be one grouping identity per cell +#' +#' @return A ggplot2 object # #' @importFrom ggplot2 ggplot aes_string geom_raster scale_fill_gradient -#' scale_fill_gradientn theme element_blank labs geom_point guides guide_legend geom_tile +#' scale_fill_gradientn theme element_blank labs geom_point guides +#' guide_legend geom_tile +#' +#' @keywords internal +#' +#' @export # SingleRasterMap <- function( data, @@ -7496,37 +7480,46 @@ SingleRasterMap <- function( return(plot) } -# Base plotting function for all Spatial plots -# -# @param data Data.frame with info to be plotted -# @param image SpatialImage object to be plotted -# @param cols Vector of colors, each color corresponds to an identity class. This may also be a single character -# or numeric value corresponding to a palette as specified by \code{\link[RColorBrewer]{brewer.pal.info}}. -# By default, ggplot2 assigns colors -# @param image.alpha Adjust the opacity of the background images. Set to 0 to -# remove. -# @param pt.alpha Adjust the opacity of the points if plotting a SpatialDimPlot -# @param crop Crop the plot in to focus on points plotted. Set to FALSE to show -# entire background image. -# @param pt.size.factor Sets the size of the points relative to spot.radius -# @param stroke Control the width of the border around the spots -# @param col.by Mapping variable for the point color -# @param alpha.by Mapping variable for the point alpha value -# @param cells.highlight A list of character or numeric vectors of cells to -# highlight. If only one group of cells desired, can simply pass a vector -# instead of a list. If set, colors selected cells to the color(s) in -# cols.highlight -# @param cols.highlight A vector of colors to highlight the cells as; ordered -# the same as the groups in cells.highlight; last color corresponds to -# unselected cells. -# @param geom Switch between normal spatial geom and geom to enable hover -# functionality -# @param na.value Color for spots with NA values - +#' Base plotting function for all Spatial plots +#' +#' @param data Data.frame with info to be plotted +#' @param image \code{SpatialImage} object to be plotted +#' @param cols Vector of colors, each color corresponds to an identity class. +#' This may also be a single character +#' or numeric value corresponding to a palette as specified by +#' \code{\link[RColorBrewer]{brewer.pal.info}}. By default, ggplot2 assigns +#' colors +#' @param image.alpha Adjust the opacity of the background images. Set to 0 to +#' remove. +#' @param pt.alpha Adjust the opacity of the points if plotting a +#' \code{SpatialDimPlot} +#' @param crop Crop the plot in to focus on points plotted. Set to \code{FALSE} +#' to show entire background image. +#' @param pt.size.factor Sets the size of the points relative to spot.radius +#' @param stroke Control the width of the border around the spots +#' @param col.by Mapping variable for the point color +#' @param alpha.by Mapping variable for the point alpha value +#' @param cells.highlight A list of character or numeric vectors of cells to +#' highlight. If only one group of cells desired, can simply pass a vector +#' instead of a list. If set, colors selected cells to the color(s) in +#' cols.highlight +#' @param cols.highlight A vector of colors to highlight the cells as; ordered +#' the same as the groups in cells.highlight; last color corresponds to +#' unselected cells. +#' @param geom Switch between normal spatial geom and geom to enable hover +#' functionality +#' @param na.value Color for spots with NA values +#' +#' @return A ggplot2 object +#' #' @importFrom tibble tibble #' @importFrom ggplot2 ggplot aes_string coord_fixed geom_point xlim ylim #' coord_cartesian labs theme_void theme scale_fill_brewer #' +#' @keywords internal +#' +#' @export +#' SingleSpatialPlot <- function( data, image, diff --git a/man/AutoPointSize.Rd b/man/AutoPointSize.Rd new file mode 100644 index 000000000..362239b04 --- /dev/null +++ b/man/AutoPointSize.Rd @@ -0,0 +1,24 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visualization.R +\name{AutoPointSize} +\alias{AutoPointSize} +\title{Automagically calculate a point size for ggplot2-based scatter plots} +\usage{ +AutoPointSize(data, raster = NULL) +} +\arguments{ +\item{data}{A data frame being passed to ggplot2} + +\item{raster}{If TRUE, point size is set to 1} +} +\value{ +The "optimal" point size for visualizing these data +} +\description{ +It happens to look good +} +\examples{ +df <- data.frame(x = rnorm(n = 10000), y = runif(n = 10000)) +AutoPointSize(data = df) + +} diff --git a/man/DimHeatmap.Rd b/man/DimHeatmap.Rd index 5a9603788..79dee9b6a 100644 --- a/man/DimHeatmap.Rd +++ b/man/DimHeatmap.Rd @@ -34,7 +34,7 @@ PCHeatmap(object, ...) \item{cells}{A list of cells to plot. If numeric, just plots the top cells.} -\item{reduction}{Which dimmensional reduction to use} +\item{reduction}{Which dimensional reduction to use} \item{disp.min}{Minimum display value (all values below are clipped)} diff --git a/man/PercentAbove.Rd b/man/PercentAbove.Rd new file mode 100644 index 000000000..403dbfe2b --- /dev/null +++ b/man/PercentAbove.Rd @@ -0,0 +1,24 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utilities.R +\name{PercentAbove} +\alias{PercentAbove} +\title{Calculate the percentage of a vector above some threshold} +\usage{ +PercentAbove(x, threshold) +} +\arguments{ +\item{x}{Vector of values} + +\item{threshold}{Threshold to use when calculating percentage} +} +\value{ +Returns the percentage of \code{x} values above the given threshold +} +\description{ +Calculate the percentage of a vector above some threshold +} +\examples{ +set.seed(42) +PercentAbove(sample(1:100, 10), 75) + +} diff --git a/man/SetQuantile.Rd b/man/SetQuantile.Rd new file mode 100644 index 000000000..598a2f6c3 --- /dev/null +++ b/man/SetQuantile.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visualization.R +\name{SetQuantile} +\alias{SetQuantile} +\title{Find the Quantile of Data} +\usage{ +SetQuantile(cutoff, data) +} +\arguments{ +\item{cutoff}{The cutoff to turn into a quantile} + +\item{data}{The data to turn find the quantile of} +} +\value{ +The numerical representation of the quantile +} +\description{ +Converts a quantile in character form to a number regarding some data. +String form for a quantile is represented as a number prefixed with +\dQuote{q}; for example, 10th quantile is \dQuote{q10} while 2nd quantile is +\dQuote{q2}. Will only take a quantile of non-zero data values +} +\examples{ +set.seed(42) +SetQuantile('q10', sample(1:100, 10)) + +} diff --git a/man/SingleCorPlot.Rd b/man/SingleCorPlot.Rd new file mode 100644 index 000000000..3fc762922 --- /dev/null +++ b/man/SingleCorPlot.Rd @@ -0,0 +1,52 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visualization.R +\name{SingleCorPlot} +\alias{SingleCorPlot} +\title{A single correlation plot} +\usage{ +SingleCorPlot( + data, + col.by = NULL, + cols = NULL, + pt.size = NULL, + smooth = FALSE, + rows.highlight = NULL, + legend.title = NULL, + na.value = "grey50", + span = NULL, + raster = NULL, + plot.cor = TRUE, + jitter = TRUE +) +} +\arguments{ +\item{data}{A data frame with two columns to be plotted} + +\item{col.by}{A vector or factor of values to color the plot by} + +\item{cols}{An optional vector of colors to use} + +\item{pt.size}{Point size for the plot} + +\item{smooth}{Make a smoothed scatter plot} + +\item{legend.title}{Optional legend title} + +\item{raster}{Convert points to raster format, default is \code{NULL} +which will automatically use raster if the number of points plotted is +greater than 100,000} + +\item{plot.cor}{...} + +\item{jitter}{Jitter for easier visualization of crowded points} + +\item{rows.highight}{A vector of rows to highlight (like cells.highlight in +\code{\link{SingleDimPlot}})} +} +\value{ +A ggplot2 object +} +\description{ +A single correlation plot +} +\keyword{internal} diff --git a/man/SingleDimPlot.Rd b/man/SingleDimPlot.Rd new file mode 100644 index 000000000..5ec9911af --- /dev/null +++ b/man/SingleDimPlot.Rd @@ -0,0 +1,80 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visualization.R +\name{SingleDimPlot} +\alias{SingleDimPlot} +\title{Plot a single dimension} +\usage{ +SingleDimPlot( + data, + dims, + col.by = NULL, + cols = NULL, + pt.size = NULL, + shape.by = NULL, + alpha.by = NULL, + order = NULL, + label = FALSE, + repel = FALSE, + label.size = 4, + cells.highlight = NULL, + cols.highlight = "#DE2D26", + sizes.highlight = 1, + na.value = "grey50", + raster = NULL +) +} +\arguments{ +\item{data}{Data to plot} + +\item{dims}{A two-length numeric vector with dimensions to use} + +\item{col.by}{...} + +\item{cols}{Vector of colors, each color corresponds to an identity class. +This may also be a single character or numeric value corresponding to a +palette as specified by \code{\link[RColorBrewer]{brewer.pal.info}}.By +default, ggplot2 assigns colors} + +\item{pt.size}{Adjust point size for plotting} + +\item{shape.by}{If NULL, all points are circles (default). You can specify +any cell attribute (that can be pulled with \code{\link{FetchData}}) +allowing for both different colors and different shapes on cells.} + +\item{alpha.by}{Mapping variable for the point alpha value} + +\item{order}{Specify the order of plotting for the idents. This can be +useful for crowded plots if points of interest are being buried. Provide +either a full list of valid idents or a subset to be plotted last (on top).} + +\item{label}{Whether to label the clusters} + +\item{repel}{Repel labels} + +\item{label.size}{Sets size of labels} + +\item{cells.highlight}{A list of character or numeric vectors of cells to +highlight. If only one group of cells desired, can simply +pass a vector instead of a list. If set, colors selected cells to the color(s) +in \code{cols.highlight} and other cells black (white if dark.theme = TRUE); +will also resize to the size(s) passed to \code{sizes.highlight}} + +\item{cols.highlight}{A vector of colors to highlight the cells as; will +repeat to the length groups in cells.highlight} + +\item{sizes.highlight}{Size of highlighted cells; will repeat to the length +groups in cells.highlight} + +\item{na.value}{Color value for NA points when using custom scale.} + +\item{raster}{Convert points to raster format, default is \code{NULL} +which will automatically use raster if the number of points plotted is +greater than 100,000} +} +\value{ +A ggplot2 object +} +\description{ +Plot a single dimension +} +\keyword{internal} diff --git a/man/SingleExIPlot.Rd b/man/SingleExIPlot.Rd new file mode 100644 index 000000000..871167769 --- /dev/null +++ b/man/SingleExIPlot.Rd @@ -0,0 +1,51 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visualization.R +\name{SingleExIPlot} +\alias{SingleExIPlot} +\title{Plot a single expression by identity on a plot} +\usage{ +SingleExIPlot( + data, + idents, + split = NULL, + type = "violin", + sort = FALSE, + y.max = NULL, + adjust = 1, + pt.size = 0, + cols = NULL, + seed.use = 42, + log = FALSE +) +} +\arguments{ +\item{data}{Data to plot} + +\item{idents}{Idents to use} + +\item{split}{Use a split violin plot} + +\item{type}{Make either a \dQuote{ridge} or \dQuote{violin} plot} + +\item{sort}{Sort identity classes (on the x-axis) by the average +expression of the attribute being potted} + +\item{y.max}{Maximum Y value to plot} + +\item{adjust}{Adjust parameter for geom_violin} + +\item{pt.size}{Size of points for violin plots} + +\item{cols}{Colors to use for plotting} + +\item{seed.use}{Random seed to use. If NULL, don't set a seed} + +\item{log}{plot Y axis on log scale} +} +\value{ +A ggplot-based Expression-by-Identity plot +} +\description{ +Plot a single expression by identity on a plot +} +\keyword{internal} diff --git a/man/SingleImageMap.Rd b/man/SingleImageMap.Rd new file mode 100644 index 000000000..9aee51ba1 --- /dev/null +++ b/man/SingleImageMap.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visualization.R +\name{SingleImageMap} +\alias{SingleImageMap} +\title{A single heatmap from base R using \code{\link[graphics]{image}}} +\usage{ +SingleImageMap(data, order = NULL, title = NULL) +} +\arguments{ +\item{data}{matrix of data to plot} + +\item{order}{optional vector of cell names to specify order in plot} + +\item{title}{Title for plot} +} +\value{ +No return, generates a base-R heatmap using \code{\link[graphics]{image}} +} +\description{ +A single heatmap from base R using \code{\link[graphics]{image}} +} +\keyword{internal} diff --git a/man/SingleRasterMap.Rd b/man/SingleRasterMap.Rd new file mode 100644 index 000000000..ded269968 --- /dev/null +++ b/man/SingleRasterMap.Rd @@ -0,0 +1,44 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visualization.R +\name{SingleRasterMap} +\alias{SingleRasterMap} +\title{A single heatmap from ggplot2 using geom_raster} +\usage{ +SingleRasterMap( + data, + raster = TRUE, + cell.order = NULL, + feature.order = NULL, + colors = PurpleAndYellow(), + disp.min = -2.5, + disp.max = 2.5, + limits = NULL, + group.by = NULL +) +} +\arguments{ +\item{data}{A matrix or data frame with data to plot} + +\item{raster}{switch between geom_raster and geom_tile} + +\item{cell.order}{...} + +\item{feature.order}{...} + +\item{colors}{A vector of colors to use} + +\item{disp.min}{Minimum display value (all values below are clipped)} + +\item{disp.max}{Maximum display value (all values above are clipped)} + +\item{limits}{A two-length numeric vector with the limits for colors on the plot} + +\item{group.by}{A vector to group cells by, should be one grouping identity per cell} +} +\value{ +A ggplot2 object +} +\description{ +A single heatmap from ggplot2 using geom_raster +} +\keyword{internal} diff --git a/man/SingleSpatialPlot.Rd b/man/SingleSpatialPlot.Rd new file mode 100644 index 000000000..de8d25c46 --- /dev/null +++ b/man/SingleSpatialPlot.Rd @@ -0,0 +1,72 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/visualization.R +\name{SingleSpatialPlot} +\alias{SingleSpatialPlot} +\title{Base plotting function for all Spatial plots} +\usage{ +SingleSpatialPlot( + data, + image, + cols = NULL, + image.alpha = 1, + pt.alpha = NULL, + crop = TRUE, + pt.size.factor = NULL, + stroke = 0.25, + col.by = NULL, + alpha.by = NULL, + cells.highlight = NULL, + cols.highlight = c("#DE2D26", "grey50"), + geom = c("spatial", "interactive", "poly"), + na.value = "grey50" +) +} +\arguments{ +\item{data}{Data.frame with info to be plotted} + +\item{image}{\code{SpatialImage} object to be plotted} + +\item{cols}{Vector of colors, each color corresponds to an identity class. +This may also be a single character +or numeric value corresponding to a palette as specified by +\code{\link[RColorBrewer]{brewer.pal.info}}. By default, ggplot2 assigns +colors} + +\item{image.alpha}{Adjust the opacity of the background images. Set to 0 to +remove.} + +\item{pt.alpha}{Adjust the opacity of the points if plotting a +\code{SpatialDimPlot}} + +\item{crop}{Crop the plot in to focus on points plotted. Set to \code{FALSE} +to show entire background image.} + +\item{pt.size.factor}{Sets the size of the points relative to spot.radius} + +\item{stroke}{Control the width of the border around the spots} + +\item{col.by}{Mapping variable for the point color} + +\item{alpha.by}{Mapping variable for the point alpha value} + +\item{cells.highlight}{A list of character or numeric vectors of cells to +highlight. If only one group of cells desired, can simply pass a vector +instead of a list. If set, colors selected cells to the color(s) in +cols.highlight} + +\item{cols.highlight}{A vector of colors to highlight the cells as; ordered +the same as the groups in cells.highlight; last color corresponds to +unselected cells.} + +\item{geom}{Switch between normal spatial geom and geom to enable hover +functionality} + +\item{na.value}{Color for spots with NA values} +} +\value{ +A ggplot2 object +} +\description{ +Base plotting function for all Spatial plots +} +\keyword{internal} From 76143b54a040900e98afff572db94e020744f463 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Tue, 14 Sep 2021 13:37:52 -0400 Subject: [PATCH 05/53] Fix SeuratObject branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 6a8d01726..9b52d4494 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -24,7 +24,7 @@ Authors@R: c( ) URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat BugReports: https://github.com/satijalab/seurat/issues -Remotes: mojaveazure/seurat-object@feat/standard +Remotes: mojaveazure/seurat-object@feat/export Depends: R (>= 4.0.0), methods From 4999fea233ae103ff6fb5b98c15a525440c0a0ac Mon Sep 17 00:00:00 2001 From: Saket Choudhary Date: Thu, 16 Sep 2021 08:22:42 -0400 Subject: [PATCH 06/53] Add docsearch to website --- NEWS.md | 4 ++-- _pkgdown.yaml | 5 +++++ 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 3a62cfac1..ae6ea3526 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# Seurat 4.0.4 (2020-08-19) +# Seurat 4.0.4 (2021-08-19) ## Added - Add `reduction` parameter to `BuildClusterTree()` ([#4598](https://github.com/satijalab/seurat/issues/4598)) - Add DensMAP option to `RunUMAP()` ([#4630](https://github.com/satijalab/seurat/pull/4630)) @@ -19,7 +19,7 @@ - Fix issue in SingleCellExperiment conversion where the mainExp would not be set properly - Fix for default dispersion info displayed in `VariableFeaturePlot()` -# Seurat 4.0.3 (2020-06-10) +# Seurat 4.0.3 (2021-06-10) ## Added - Add `jitter` parameter to `FeatureScatter()` diff --git a/_pkgdown.yaml b/_pkgdown.yaml index 4f2139554..2beb7fc74 100644 --- a/_pkgdown.yaml +++ b/_pkgdown.yaml @@ -1,9 +1,14 @@ +url: https://satijalab.org/seurat + destination: docs template: params: bootswatch: flatly ganalytics: UA-82807227-1 + docsearch: + api_key: ead918d7fe8467a2fd38e97f5bbe3ecb + index_name: seurat navbar: title: "Seurat" From b1db6d8f1b6050bc5358c34c1031c2c9276c8d70 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Thu, 7 Oct 2021 11:43:09 -0400 Subject: [PATCH 07/53] not center query lsi embeddings --- R/integration.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/integration.R b/R/integration.R index 81c34006b..62150ed1b 100644 --- a/R/integration.R +++ b/R/integration.R @@ -1041,7 +1041,7 @@ FindTransferAnchors <- function( reduction = query[[reference.reduction]], data = GetAssayData(object = reference, assay = reference.assay, slot = "data"), mode = "lsi", - do.center = TRUE, + do.center = FALSE, do.scale = FALSE, use.original.stats = FALSE, verbose = verbose @@ -1053,7 +1053,7 @@ FindTransferAnchors <- function( reduction = reference[[reference.reduction]], data = GetAssayData(object = query, assay = query.assay, slot = "data"), mode = "lsi", - do.center = TRUE, + do.center = FALSE, do.scale = FALSE, use.original.stats = FALSE, verbose = verbose From 07383a0ed9553b8bca544723b24ea354f62a80c1 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Thu, 7 Oct 2021 11:51:55 -0400 Subject: [PATCH 08/53] add News --- NEWS.md | 1 + 1 file changed, 1 insertion(+) diff --git a/NEWS.md b/NEWS.md index 8fcea6c95..2d897c06b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -13,6 +13,7 @@ - Add `ReadParsebio()` function to read output from Parse Biosciences - Add the `image.alpha` parameter to `SpatialDimPlot()` and `SpatialFeaturePlot()` - Add support for the correlation metric in `RunUMAP` ([#4972](https://github.com/satijalab/seurat/issues/4972)) +- Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors` ## Changes - Warn and continue rather than erroring if not all features are available in `FindSpatiallyVariableFeatures()` ([#4611](https://github.com/satijalab/seurat/issues/4611)) From 297764caa21957255631a157049c88e1167a2e01 Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Thu, 7 Oct 2021 14:14:14 -0400 Subject: [PATCH 09/53] Update dev version --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ff8a7108f..1d948cb18 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Seurat -Version: 4.0.4.9002 -Date: 2021-09-10 +Version: 4.0.4.9003 +Date: 2021-10-07 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. Authors@R: c( From 8b747004631e7e257f2cf76ca1ea838b83b3c232 Mon Sep 17 00:00:00 2001 From: Saket Choudhary Date: Fri, 8 Oct 2021 12:27:49 -0400 Subject: [PATCH 10/53] Fix readmtx error message --- DESCRIPTION | 2 +- NEWS.md | 1 + R/preprocessing.R | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1d948cb18..19405f10d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: Seurat -Version: 4.0.4.9003 +Version: 4.0.4.9004 Date: 2021-10-07 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. diff --git a/NEWS.md b/NEWS.md index 2d897c06b..47d33b05b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,7 @@ ## Changes - Update documentation for `to.upper` parameter in `Load10X_Spatial()` ([#4576](https://github.com/satijalab/seurat/issues/4576)) - Update concept tags for `RunSPCA()` ([#4978](https://github.com/satijalab/seurat/discussions/4987)) +- Fix error message in `ReadMtx()` ([#5158]https://github.com/satijalab/seurat/issues/5158)) ## Seurat 4.0.4 (2020-08-19) ## Added diff --git a/R/preprocessing.R b/R/preprocessing.R index 335dd78d4..6e9363c41 100644 --- a/R/preprocessing.R +++ b/R/preprocessing.R @@ -1224,7 +1224,7 @@ ReadMtx <- function( if (length(x = feature.names) != nrow(x = data)) { stop( "Matrix has ", - ncol(data), + nrow(data), " rows but found ", length(feature.names), " features. ", ifelse( From 43a0469f366cc790afc8415c09c230d9f843c744 Mon Sep 17 00:00:00 2001 From: Saket Choudhary Date: Fri, 8 Oct 2021 12:29:21 -0400 Subject: [PATCH 11/53] Fix news --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 47d33b05b..3b031ff4c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,7 +2,7 @@ ## Changes - Update documentation for `to.upper` parameter in `Load10X_Spatial()` ([#4576](https://github.com/satijalab/seurat/issues/4576)) - Update concept tags for `RunSPCA()` ([#4978](https://github.com/satijalab/seurat/discussions/4987)) -- Fix error message in `ReadMtx()` ([#5158]https://github.com/satijalab/seurat/issues/5158)) +- Fix error message in `ReadMtx()` ([#5158](https://github.com/satijalab/seurat/issues/5158)) ## Seurat 4.0.4 (2020-08-19) ## Added From 675e20b646bc8ff94636a180e65e66820ee30332 Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Fri, 22 Oct 2021 12:25:37 -0400 Subject: [PATCH 12/53] Fix version history --- NEWS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 48100630f..901ebb548 100644 --- a/NEWS.md +++ b/NEWS.md @@ -3,12 +3,12 @@ ## Changes - Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors` +- Fix error message in `ReadMtx()` ([#5158](https://github.com/satijalab/seurat/issues/5158)) # Seurat 4.0.5 (2020-10-04) ## Changes - Update documentation for `to.upper` parameter in `Load10X_Spatial()` ([#4576](https://github.com/satijalab/seurat/issues/4576)) - Update concept tags for `RunSPCA()` ([#4978](https://github.com/satijalab/seurat/discussions/4987)) -- Fix error message in `ReadMtx()` ([#5158](https://github.com/satijalab/seurat/issues/5158)) - Conditionally run tests/packages that use suggested packages ([#5160](https://github.com/satijalab/seurat/pull/5160)) # Seurat 4.0.4 (2020-08-19) From 025b4c0b825cf9e1649913a2d40c8e99a66f0e33 Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Fri, 22 Oct 2021 14:20:18 -0400 Subject: [PATCH 13/53] Set random state in umap-learn method; #5194 --- R/dimensional_reduction.R | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 322ff6880..19535d4bf 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -1265,6 +1265,9 @@ RunUMAP.default <- function( if (!py_module_available(module = 'umap')) { stop("Cannot find UMAP, please install through pip (e.g. pip install umap-learn).") } + if (!py_module_available(module = 'sklearn')) { + stop("Cannot find sklearn, please install through pip (e.g. pip install scikit-learn).") + } if (!is.null(x = seed.use)) { py_set_seed(seed = seed.use) } @@ -1272,11 +1275,13 @@ RunUMAP.default <- function( n.epochs <- as.integer(x = n.epochs) } umap_import <- import(module = "umap", delay_load = TRUE) + sklearn <- import("sklearn", delay_load = TRUE) if (densmap && numeric_version(x = umap_import$pkg_resources$get_distribution("umap-learn")$version) < numeric_version(x = "0.5.0")) { stop("densmap is only supported by versions >= 0.5.0 of umap-learn. Upgrade umap-learn (e.g. pip install --upgrade umap-learn).") } + random.state <- sklearn$utils$check_random_state(seed = as.integer(x = seed.use)) umap.args <- list( n_neighbors = as.integer(x = n.neighbors), n_components = as.integer(x = n.components), @@ -1289,6 +1294,7 @@ RunUMAP.default <- function( local_connectivity = local.connectivity, repulsion_strength = repulsion.strength, negative_sample_rate = negative.sample.rate, + random_state = random.state, a = a, b = b, metric_kwds = metric.kwds, From 3bcc0ed602ca100fa1d686f7bc1952b567211bc1 Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Fri, 22 Oct 2021 14:21:59 -0400 Subject: [PATCH 14/53] Update release notes --- DESCRIPTION | 4 ++-- NEWS.md | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f34ee9f4a..ad567de6e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Seurat -Version: 4.0.5.9000 -Date: 2021-10-19 +Version: 4.0.5.9001 +Date: 2021-10-22 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 5ea47d791..70a5771d0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -9,6 +9,7 @@ - Update documentation for `to.upper` parameter in `Load10X_Spatial()` ([#4576](https://github.com/satijalab/seurat/issues/4576)) - Update concept tags for `RunSPCA()` ([#4978](https://github.com/satijalab/seurat/discussions/4987)) - Conditionally run tests/packages that use suggested packages ([#5160](https://github.com/satijalab/seurat/pull/5160)) +- Set random state in `RunUMAP()` when using the `umap-learn` method ([#5194](https://github.com/satijalab/seurat/issues/5194)) # Seurat 4.0.4 (2020-08-19) ## Added From 22b29ff654e218146262eac4a9eb5c2b4751e1f8 Mon Sep 17 00:00:00 2001 From: Saket Choudhary Date: Thu, 28 Oct 2021 10:37:51 -0400 Subject: [PATCH 15/53] Update NEWS; document --- DESCRIPTION | 2 +- NEWS.md | 1 + man/FindConservedMarkers.Rd | 3 +++ 3 files changed, 5 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ad567de6e..6b8fdfc9f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: Seurat -Version: 4.0.5.9001 +Version: 4.0.5.9002 Date: 2021-10-22 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. diff --git a/NEWS.md b/NEWS.md index 35b40a28b..59a4570e7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,7 @@ ## Added ## Changes +- Add `min.cells.group` parameter to `FindConservedMarkers` ([#5079](https://github.com/satijalab/seurat/pull/5079)) - Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors` - Fix error message in `ReadMtx()` ([#5158](https://github.com/satijalab/seurat/issues/5158)) diff --git a/man/FindConservedMarkers.Rd b/man/FindConservedMarkers.Rd index f8595291a..429c7dd9e 100644 --- a/man/FindConservedMarkers.Rd +++ b/man/FindConservedMarkers.Rd @@ -11,6 +11,7 @@ FindConservedMarkers( grouping.var, assay = "RNA", slot = "data", + min.cells.group = 3, meta.method = metap::minimump, verbose = TRUE, ... @@ -31,6 +32,8 @@ use all other cells for comparison.} \item{slot}{Slot to pull data from; note that if \code{test.use} is "negbinom", "poisson", or "DESeq2", \code{slot} will be set to "counts"} +\item{min.cells.group}{Minimum number of cells in one of the groups} + \item{meta.method}{method for combining p-values. Should be a function from the metap package (NOTE: pass the function, not a string)} From f192912fa45d7495b3e2110d88397febb90581f6 Mon Sep 17 00:00:00 2001 From: Saket Choudhary Date: Thu, 28 Oct 2021 12:59:27 -0400 Subject: [PATCH 16/53] Make ggrastr based rasterization optional --- DESCRIPTION | 1 - R/visualization.R | 33 +++++++++++++++++++++------------ man/VlnPlot.Rd | 5 ++++- 3 files changed, 25 insertions(+), 14 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0f0ce172c..ad567de6e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -34,7 +34,6 @@ Imports: future, future.apply, ggplot2 (>= 3.3.0), - ggrastr, ggrepel, ggridges, graphics, diff --git a/R/visualization.R b/R/visualization.R index 450c74acf..d751cae51 100644 --- a/R/visualization.R +++ b/R/visualization.R @@ -554,8 +554,9 @@ RidgePlot <- function( #' single violin shapes. #' @param adjust Adjust parameter for geom_violin #' @param flip flip plot orientation (identities on x-axis) -#' @param raster Convert points to raster format, default is \code{NULL} which -#' automatically rasterizes if plotting more than 100,000 cells +#' @param raster Convert points to raster format. Requires 'ggrastr' to be installed. +# default is \code{NULL} which automatically rasterizes if ggrastr is installed and +# number of points exceed 100,000. #' #' @return A \code{\link[patchwork]{patchwork}ed} ggplot object if #' \code{combine = TRUE}; otherwise, a list of ggplot objects @@ -7230,8 +7231,9 @@ SingleDimPlot <- function( # @param cols Colors to use for plotting # @param log plot Y axis on log scale # @param seed.use Random seed to use. If NULL, don't set a seed -# @param raster Convert points to raster format, default is \code{NULL} which -# automatically rasterizes if plotting more than 100,000 cells +# @param raster Convert points to raster format. Requires 'ggrastr' to be installed. +# default is \code{NULL} which automatically rasterizes if ggrastr is installed and +# number of points exceed 100,000. # # @return A ggplot-based Expression-by-Identity plot # @@ -7240,7 +7242,6 @@ SingleDimPlot <- function( #' @importFrom utils globalVariables #' @importFrom ggridges geom_density_ridges theme_ridges #' @importFrom ggplot2 ggplot aes_string theme labs geom_violin geom_jitter ylim position_jitterdodge -#' @importFrom ggrastr rasterize #' scale_fill_manual scale_y_log10 scale_x_log10 scale_y_discrete scale_x_continuous waiver #' @importFrom cowplot theme_cowplot #' @@ -7258,12 +7259,20 @@ SingleExIPlot <- function( log = FALSE, raster = NULL ) { - if ((nrow(x = data) > 1e5) & !isFALSE(raster)){ - message("Rasterizing points since number of points exceeds 100,000.", - "\nTo disable this behavior set `raster=FALSE`") + if (!is.null(x = raster) && isTRUE(x = raster)){ + if (!PackageCheck('ggrastr', error = FALSE)) { + stop("Please install ggrastr from CRAN to enable rasterization.") + } + } + if (PackageCheck('ggrastr', error = FALSE)) { + # Set rasterization to true if ggrastr is installed and + # number of points exceeds 100,000 + if ((nrow(x = data) > 1e5) & !isFALSE(raster)){ + message("Rasterizing points since number of points exceeds 100,000.", + "\nTo disable this behavior set `raster=FALSE`") + } + raster <- TRUE } - raster <- raster %||% (nrow(x = data) > 1e5) - if (!is.null(x = seed.use)) { set.seed(seed = seed.use) @@ -7325,13 +7334,13 @@ SingleExIPlot <- function( ) if (is.null(x = split)) { if (isTRUE(x = raster)) { - jitter <- rasterize(geom_jitter(height = 0, size = pt.size, show.legend = FALSE)) + jitter <- ggrastr::rasterize(geom_jitter(height = 0, size = pt.size, show.legend = FALSE)) } else { jitter <- geom_jitter(height = 0, size = pt.size, show.legend = FALSE) } } else { if (isTRUE(x = raster)) { - jitter <- rasterize(geom_jitter( + jitter <- ggrastr::rasterize(geom_jitter( position = position_jitterdodge(jitter.width = 0.4, dodge.width = 0.9), size = pt.size, show.legend = FALSE diff --git a/man/VlnPlot.Rd b/man/VlnPlot.Rd index c2ed98302..75a30f331 100644 --- a/man/VlnPlot.Rd +++ b/man/VlnPlot.Rd @@ -24,7 +24,8 @@ VlnPlot( stack = FALSE, combine = TRUE, fill.by = "feature", - flip = FALSE + flip = FALSE, + raster = NULL ) } \arguments{ @@ -71,6 +72,8 @@ ggplot object. If \code{FALSE}, return a list of ggplot} \item{fill.by}{Color violins/ridges based on either 'feature' or 'ident'} \item{flip}{flip plot orientation (identities on x-axis)} + +\item{raster}{Convert points to raster format. Requires 'ggrastr' to be installed.} } \value{ A \code{\link[patchwork]{patchwork}ed} ggplot object if From 7f3612c1f4990e8cc185a537f682c8daebece266 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Tue, 2 Nov 2021 11:36:47 -0400 Subject: [PATCH 17/53] supervised LSI --- R/dimensional_reduction.R | 49 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 19535d4bf..012cd8083 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -2425,3 +2425,52 @@ RunSPCA.Seurat <- function( object <- LogSeuratCommand(object = object) return(object) } + + + +## run supervised LSI +## +RunSLSI <- function(object, + assay = NULL, + graph, + npc = 50, + project = TRUE, + reduction.name = "slsi", + reduction.key = "SLSI_", + verbose = TRUE +) { + assay <- assay %||% DefaultAssay(object) + X <- GetAssayData(object, assay = assay) + if (verbose) { + message("Smoothing peaks matrix") + } + XTX.smooth <- t(graph) %*% (t(X) %*% X) %*% graph + if (verbose) { + message("Running eigendecomposition") + } + svd.V <- irlba(A = XTX.smooth, nv = npc, nu = npc) + sigma <- sqrt(x = svd.V$d) + feature.loadings <- X %*% (graph %*% svd.V$u) %*% diag(x = 1/sigma) + feature.loadings <- as.matrix(x = feature.loadings) + if (project) { + cell.embeddings <- t(X) %*% feature.loadings %*% diag(x = 1/sigma) + } else { + cell.embeddings <- svd.V$u + } + cell.embeddings <- as.matrix(x = cell.embeddings) + + # construct svd list stored in misc for LSI projection + svd.lsi <- svd.V + svd.lsi$d <- sigma + svd.lsi$u <- feature.loadings + svd.lsi$v <- cell.embeddings + + colnames(x = cell.embeddings) <- paste0(reduction.key, 1:ncol(cell.embeddings)) + object[[reduction.name]] <- CreateDimReducObject(embeddings = cell.embeddings, + loadings = feature.loadings, + key = reduction.key, + assay = assay, + misc = svd.lsi + ) + return(object) +} From 7845be2086200014f4ff30696df0c9af5847d3cd Mon Sep 17 00:00:00 2001 From: Saket Choudhary Date: Tue, 2 Nov 2021 21:44:04 -0400 Subject: [PATCH 18/53] Suggests: ggrastr --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ad567de6e..ce8135f95 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -119,4 +119,5 @@ Suggests: limma, metap, enrichR, - mixtools + mixtools, + ggrastr From b11c89a8571962da2d1d13864d1b2243023cf15c Mon Sep 17 00:00:00 2001 From: Saket Choudhary Date: Tue, 2 Nov 2021 21:49:23 -0400 Subject: [PATCH 19/53] Update NEWS; bump version --- DESCRIPTION | 2 +- NEWS.md | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index b32cee440..187b5051e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: Seurat -Version: 4.0.5.9002 +Version: 4.0.5.9003 Date: 2021-10-22 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. diff --git a/NEWS.md b/NEWS.md index 59a4570e7..4e0db768a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,6 +2,7 @@ ## Added ## Changes +- Add `raster` parameter to `VlnPlot` to optionally rasterize individual points ([#5076](https://github.com/satijalab/seurat/pull/5076)) - Add `min.cells.group` parameter to `FindConservedMarkers` ([#5079](https://github.com/satijalab/seurat/pull/5079)) - Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors` - Fix error message in `ReadMtx()` ([#5158](https://github.com/satijalab/seurat/issues/5158)) From eab3ed70c15e9c8f7cb932a6ce2e5d516dcad74d Mon Sep 17 00:00:00 2001 From: samuel-marsh Date: Fri, 19 Nov 2021 10:05:27 -0500 Subject: [PATCH 20/53] add label.color param --- R/visualization.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/R/visualization.R b/R/visualization.R index 25d74c015..cf68bbf5d 100644 --- a/R/visualization.R +++ b/R/visualization.R @@ -979,6 +979,7 @@ FeaturePlot <- function( blend.threshold = 0.5, label = FALSE, label.size = 4, + label.color = "black", repel = FALSE, ncol = NULL, coord.fixed = FALSE, @@ -1261,7 +1262,8 @@ FeaturePlot <- function( plot = plot, id = 'ident', repel = repel, - size = label.size + size = label.size, + color = label.color ) } # Make FeatureHeatmaps look nice(ish) From dea33bb6a5fdb9ba1746e10eb86c45c161a744a4 Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Fri, 19 Nov 2021 14:00:03 -0500 Subject: [PATCH 21/53] Add reexports to website --- R/reexports.R | 66 +++++++-------------------------------------------- _pkgdown.yaml | 5 ++++ 2 files changed, 13 insertions(+), 58 deletions(-) diff --git a/R/reexports.R b/R/reexports.R index 29820e40b..0763d0a0b 100644 --- a/R/reexports.R +++ b/R/reexports.R @@ -146,349 +146,299 @@ NULL #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% #' @importFrom SeuratObject AddMetaData -#' @rdname reexports #' @export #' SeuratObject::AddMetaData #' @importFrom SeuratObject as.Graph -#' @rdname reexports #' @export #' SeuratObject::as.Graph #' @importFrom SeuratObject as.Neighbor -#' @rdname reexports #' @export #' SeuratObject::as.Neighbor #' @importFrom SeuratObject as.Seurat -#' @rdname reexports #' @export #' SeuratObject::as.Seurat #' @importFrom SeuratObject as.sparse -#' @rdname reexports #' @export #' SeuratObject::as.sparse #' @importFrom SeuratObject Assays -#' @rdname reexports #' @export #' SeuratObject::Assays #' @importFrom SeuratObject Cells -#' @rdname reexports #' @export #' SeuratObject::Cells #' @importFrom SeuratObject CellsByIdentities -#' @rdname reexports #' @export #' SeuratObject::CellsByIdentities #' @importFrom SeuratObject Command -#' @rdname reexports + #' @export #' SeuratObject::Command #' @importFrom SeuratObject CreateAssayObject -#' @rdname reexports + #' @export #' SeuratObject::CreateAssayObject #' @importFrom SeuratObject CreateDimReducObject -#' @rdname reexports #' @export #' SeuratObject::CreateDimReducObject #' @importFrom SeuratObject CreateSeuratObject -#' @rdname reexports + #' @export #' SeuratObject::CreateSeuratObject #' @importFrom SeuratObject DefaultAssay -#' @rdname reexports #' @export #' SeuratObject::DefaultAssay #' @importFrom SeuratObject DefaultAssay<- -#' @rdname reexports #' @export #' SeuratObject::`DefaultAssay<-` #' @importFrom SeuratObject Distances -#' @rdname reexports #' @export #' SeuratObject::Distances #' @importFrom SeuratObject Embeddings -#' @rdname reexports #' @export #' SeuratObject::Embeddings #' @importFrom SeuratObject FetchData -#' @rdname reexports #' @export #' SeuratObject::FetchData #' @importFrom SeuratObject GetAssayData -#' @rdname reexports #' @export #' SeuratObject::GetAssayData #' @importFrom SeuratObject GetImage -#' @rdname reexports #' @export #' SeuratObject::GetImage #' @importFrom SeuratObject GetTissueCoordinates -#' @rdname reexports #' @export #' SeuratObject::GetTissueCoordinates #' @importFrom SeuratObject HVFInfo -#' @rdname reexports #' @export #' SeuratObject::HVFInfo #' @importFrom SeuratObject Idents -#' @rdname reexports #' @export #' SeuratObject::Idents #' @importFrom SeuratObject Idents<- -#' @rdname reexports #' @export #' SeuratObject::`Idents<-` #' @importFrom SeuratObject Images -#' @rdname reexports #' @export #' SeuratObject::Images #' @importFrom SeuratObject Index -#' @rdname reexports #' @export #' SeuratObject::Index #' @importFrom SeuratObject Index<- -#' @rdname reexports #' @export #' SeuratObject::`Index<-` #' @importFrom SeuratObject Indices -#' @rdname reexports #' @export #' SeuratObject::Indices #' @importFrom SeuratObject IsGlobal -#' @rdname reexports #' @export #' SeuratObject::IsGlobal #' @importFrom SeuratObject JS -#' @rdname reexports #' @export #' SeuratObject::JS #' @importFrom SeuratObject JS<- -#' @rdname reexports + #' @export #' SeuratObject::`JS<-` #' @importFrom SeuratObject Key -#' @rdname reexports #' @export #' SeuratObject::Key #' @importFrom SeuratObject Key<- -#' @rdname reexports + #' @export #' SeuratObject::`Key<-` #' @importFrom SeuratObject Loadings -#' @rdname reexports + #' @export #' SeuratObject::Loadings #' @importFrom SeuratObject Loadings<- -#' @rdname reexports #' @export #' SeuratObject::`Loadings<-` #' @importFrom SeuratObject LogSeuratCommand -#' @rdname reexports + #' @export #' SeuratObject::LogSeuratCommand #' @importFrom SeuratObject Misc -#' @rdname reexports #' @export #' SeuratObject::Misc #' @importFrom SeuratObject Misc<- -#' @rdname reexports #' @export #' SeuratObject::`Misc<-` #' @importFrom SeuratObject Neighbors -#' @rdname reexports #' @export #' SeuratObject::Neighbors #' @importFrom SeuratObject Project -#' @rdname reexports #' @export #' SeuratObject::Project #' @importFrom SeuratObject Project<- -#' @rdname reexports #' @export #' SeuratObject::`Project<-` #' @importFrom SeuratObject Radius -#' @rdname reexports #' @export #' SeuratObject::Radius #' @importFrom SeuratObject Reductions -#' @rdname reexports #' @export #' SeuratObject::Reductions #' @importFrom SeuratObject RenameCells -#' @rdname reexports #' @export #' SeuratObject::RenameCells #' @importFrom SeuratObject RenameIdents -#' @rdname reexports #' @export #' SeuratObject::RenameIdents #' @importFrom SeuratObject ReorderIdent -#' @rdname reexports #' @export #' SeuratObject::ReorderIdent #' @importFrom SeuratObject RowMergeSparseMatrices -#' @rdname reexports #' @export #' SeuratObject::RowMergeSparseMatrices #' @importFrom SeuratObject SetAssayData -#' @rdname reexports #' @export #' SeuratObject::SetAssayData #' @importFrom SeuratObject SetIdent -#' @rdname reexports #' @export #' SeuratObject::SetIdent #' @importFrom SeuratObject SpatiallyVariableFeatures -#' @rdname reexports #' @export #' SeuratObject::SpatiallyVariableFeatures #' @importFrom SeuratObject StashIdent -#' @rdname reexports #' @export #' SeuratObject::StashIdent #' @importFrom SeuratObject Stdev -#' @rdname reexports #' @export #' SeuratObject::Stdev #' @importFrom SeuratObject SVFInfo -#' @rdname reexports #' @export #' SeuratObject::SVFInfo #' @importFrom SeuratObject Tool -#' @rdname reexports #' @export #' SeuratObject::Tool #' @importFrom SeuratObject Tool<- -#' @rdname reexports #' @export #' SeuratObject::`Tool<-` #' @importFrom SeuratObject UpdateSeuratObject -#' @rdname reexports #' @export #' SeuratObject::UpdateSeuratObject #' @importFrom SeuratObject VariableFeatures -#' @rdname reexports + #' @export #' SeuratObject::VariableFeatures #' @importFrom SeuratObject VariableFeatures<- -#' @rdname reexports #' @export #' SeuratObject::`VariableFeatures<-` #' @importFrom SeuratObject WhichCells -#' @rdname reexports #' @export #' SeuratObject::WhichCells diff --git a/_pkgdown.yaml b/_pkgdown.yaml index 4f2139554..9eafa3a0d 100644 --- a/_pkgdown.yaml +++ b/_pkgdown.yaml @@ -149,3 +149,8 @@ reference: desc: "Functions included for user convenience and to keep maintain backwards compatability" - contents: - has_concept("convenience") + +- title: "Re-exports" + desc: "Functions re-exported from other packages" +- contents: + - reexports From c2941a1fa2a831b8040db7f0e2dea0bcb0abdd5b Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Fri, 19 Nov 2021 14:23:30 -0500 Subject: [PATCH 22/53] Update extensions page --- vignettes/extensions.Rmd | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/vignettes/extensions.Rmd b/vignettes/extensions.Rmd index 74a1bfb06..787bdcdb6 100644 --- a/vignettes/extensions.Rmd +++ b/vignettes/extensions.Rmd @@ -7,7 +7,7 @@ In addition to the core Seurat package, we provide several extensions that enhan # Signac -Signac is an R toolkit that extends Seurat for the analysis, interpretation, and exploration of single-cell chromatin datasets. Currently in active development, the software supports the following features: +Signac is an R toolkit that extends Seurat for the analysis, interpretation, and exploration of single-cell chromatin datasets. The software supports the following features: * Calculating single-cell QC metrics * Dimensional reduction, visualization, and clustering @@ -24,3 +24,12 @@ SeuratData is a mechanism for distributing datasets in the form of Seurat object # SeuratWrappers In order to facilitate the use of community tools with Seurat, we provide the SeuratWrappers package, which contains code to run other analysis tools on Seurat objects. For a full list of supported packages and vignettes, please see our vignettes page. + +# SeuratDisk + +The SeuratDisk package introduces the h5Seurat file format for the storage and analysis of multimodal single-cell and spatially-resolved expression experiments. The SeuratDisk package provides functions to save Seurat objects as h5Seurat files, and functions for rapid on-disk conversion between h5Seurat and AnnData formats with the goal of enhancing interoperability between Seurat and Scanpy. For more information, click [here](https://mojaveazure.github.io/seurat-disk/) + +# Azimuth + +Azimuth is a web application that uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix of gene expression in single cells, and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery). All results can be explored within the app, and easily downloaded for additional downstream analysis. To use the Azimuth web app, visit the Azimuth website [here](https://azimuth.hubmapconsortium.org/). + From 4f713af36b318071973fc6c3e96eefc394d26fd8 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Mon, 22 Nov 2021 08:55:49 -0500 Subject: [PATCH 23/53] update slsi --- NAMESPACE | 5 ++ R/dimensional_reduction.R | 159 ++++++++++++++++++++++++++++++++------ R/generics.R | 30 ++++++- 3 files changed, 169 insertions(+), 25 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index c847f2c78..5c3ca7270 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -69,6 +69,9 @@ S3method(RunLDA,default) S3method(RunPCA,Assay) S3method(RunPCA,Seurat) S3method(RunPCA,default) +S3method(RunSLSI,Assay) +S3method(RunSLSI,Seurat) +S3method(RunSLSI,default) S3method(RunSPCA,Assay) S3method(RunSPCA,Seurat) S3method(RunSPCA,default) @@ -284,6 +287,7 @@ export(RunMarkVario) export(RunMixscape) export(RunMoransI) export(RunPCA) +export(RunSLSI) export(RunSPCA) export(RunTSNE) export(RunUMAP) @@ -438,6 +442,7 @@ importFrom(SeuratObject,as.Graph) importFrom(SeuratObject,as.Neighbor) importFrom(SeuratObject,as.Seurat) importFrom(SeuratObject,as.sparse) +importFrom(sparseMatrixStats, rowVars) importFrom(cluster,clara) importFrom(cowplot,get_legend) importFrom(cowplot,plot_grid) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 012cd8083..2f7589f19 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -2260,18 +2260,19 @@ L2Norm <- function(vec) { # @param features Features to use as input for the dimensional reduction technique. # Default is variable features # @ param verbose Print messages and warnings -# +# @importFrom sparseMatrixStats rowVars # PrepDR <- function( object, features = NULL, + slot = 'scale.data', verbose = TRUE ) { if (length(x = VariableFeatures(object = object)) == 0 && is.null(x = features)) { stop("Variable features haven't been set. Run FindVariableFeatures() or provide a vector of feature names.") } - data.use <- GetAssayData(object = object, slot = "scale.data") - if (nrow(x = data.use ) == 0) { + data.use <- GetAssayData(object = object, slot = slot) + if (nrow(x = data.use ) == 0 && slot == "scale.data") { stop("Data has not been scaled. Please run ScaleData and retry") } features <- features %||% VariableFeatures(object = object) @@ -2283,7 +2284,13 @@ PrepDR <- function( } } features <- features.keep - features.var <- apply(X = data.use[features, ], MARGIN = 1, FUN = var) + + if (inherits(x = data.use, what = 'dgCMatrix')) { + features.var <- rowVars(x = data.use[features, ]) + } + else { + features.var <- RowVar(x = data.use[features, ]) + } features.keep <- features[features.var > 0] if (length(x = features.keep) < length(x = features)) { features.exclude <- setdiff(x = features, y = features.keep) @@ -2427,35 +2434,53 @@ RunSPCA.Seurat <- function( } - -## run supervised LSI -## -RunSLSI <- function(object, - assay = NULL, - graph, - npc = 50, - project = TRUE, - reduction.name = "slsi", - reduction.key = "SLSI_", - verbose = TRUE +#' @param assay Name of Assay SLSI is being run on +#' @param npcs Total Number of SLSIs to compute and store (50 by default) +#' @param verbose Print the top genes associated with high/low loadings for +#' the SLSIs +#' @param reduction.key dimensional reduction key, specifies the string before +#' the number for the dimension names. SLSI by default +#' @param graph Graph used supervised by SLSI +#' @param seed.use Set a random seed. By default, sets the seed to 42. Setting +#' NULL will not set a seed. +#' +#' @importFrom irlba irlba +#' +#' @concept dimensional_reduction +#' @rdname RunSLSI +#' @export +RunSLSI.default <- function( + object, + assay = NULL, + nlsi = 50, + reduction.key = "SLSI_", + graph = NULL, + verbose = TRUE, + project = TRUE, + seed.use = 42, + ... ) { - assay <- assay %||% DefaultAssay(object) - X <- GetAssayData(object, assay = assay) + if (!is.null(x = seed.use)) { + set.seed(seed = seed.use) + } + nlsi <- min(nlsi, nrow(x = object) - 1) + if (verbose) { message("Smoothing peaks matrix") } - XTX.smooth <- t(graph) %*% (t(X) %*% X) %*% graph + object.smooth <- t(graph) %*% (t(object) %*% object) %*% graph if (verbose) { - message("Running eigendecomposition") + message("Performing eigendecomposition") } - svd.V <- irlba(A = XTX.smooth, nv = npc, nu = npc) + svd.V <- irlba(A = object.smooth, nv = nlsi, nu = nlsi) sigma <- sqrt(x = svd.V$d) - feature.loadings <- X %*% (graph %*% svd.V$u) %*% diag(x = 1/sigma) + feature.loadings <- object %*% (graph %*% svd.V$u) %*% diag(x = 1/sigma) feature.loadings <- as.matrix(x = feature.loadings) if (project) { - cell.embeddings <- t(X) %*% feature.loadings %*% diag(x = 1/sigma) + cell.embeddings <- t(object) %*% feature.loadings %*% diag(x = 1/sigma) } else { cell.embeddings <- svd.V$u + rownames(cell.embeddings) <- colnames(object) } cell.embeddings <- as.matrix(x = cell.embeddings) @@ -2466,11 +2491,97 @@ RunSLSI <- function(object, svd.lsi$v <- cell.embeddings colnames(x = cell.embeddings) <- paste0(reduction.key, 1:ncol(cell.embeddings)) - object[[reduction.name]] <- CreateDimReducObject(embeddings = cell.embeddings, + reduction.data <- CreateDimReducObject(embeddings = cell.embeddings, loadings = feature.loadings, key = reduction.key, assay = assay, misc = svd.lsi - ) + ) + return(reduction.data) +} + + + + +#' @param features Features to compute SLSI on. If features=NULL, SLSI will be run +#' using the variable features for the Assay. +#' +#' @rdname RunSLSI +#' @concept dimensional_reduction +#' @export +#' @method RunSPCA Assay +#' +RunSLSI.Assay <- function( + object, + assay = NULL, + features = NULL, + nlsi = 50, + reduction.key = "SLSI_", + graph = NULL, + verbose = TRUE, + seed.use = 42, + ... +) { + data.use <- PrepDR( + object = object, + features = features, + slot = "data", + verbose = verbose + ) + reduction.data <- RunSLSI( + object = data.use, + assay = assay, + nlsi = nlsi, + reduction.key = reduction.key, + graph = graph, + verbose = verbose, + seed.use = seed.use, + ... + ) + return(reduction.data) +} + + + + +#' @param reduction.name dimensional reduction name, spca by default +#' @rdname RunSLSI +#' @concept dimensional_reduction +#' @export +#' @method RunSLSI Seurat +#' +RunSLSI.Seurat <- function( + object, + assay = NULL, + features = NULL, + nlsi = 50, + reduction.name = "slsi", + reduction.key = "SLSI_", + graph = NULL, + verbose = TRUE, + seed.use = 42, + ... +) { + assay <- assay %||% DefaultAssay(object = object) + assay.data <- GetAssay(object = object, assay = assay) + if (is.null(x = graph)) { + stop("Graph is not provided") + } else if (is.character(x = graph)) { + graph <- object[[graph]] + } + reduction.data <- RunSLSI( + object = assay.data, + assay = assay, + features = features, + nlsi = nlsi, + reduction.name = reduction.name, + reduction.key = reduction.key, + graph = graph, + verbose = verbose, + seed.use = seed.use, + ... + ) + object[[reduction.name]] <- reduction.data + object <- LogSeuratCommand(object = object) return(object) } diff --git a/R/generics.R b/R/generics.R index ba893f0df..e8d04e955 100644 --- a/R/generics.R +++ b/R/generics.R @@ -441,9 +441,37 @@ RunPCA <- function(object, ...) { UseMethod(generic = 'RunPCA', object = object) } + + +#' Run Supervised Latent Semantic Indexing +#' +#' Run a supervised LSI (SLSI) dimensionality reduction supervised by a cell-cell kernel. +#' SLSI is used to capture a linear transformation which maximizes its dependency to +#' the given cell-cell kernel. +#' +#' @param object An object +#' @param ... Arguments passed to other methods and IRLBA +#' +#' @return Returns Seurat object with the SPCA calculation stored in the reductions slot +#' @references Barshan E, Ghodsi A, Azimifar Z, Jahromi MZ. +#' Supervised principal component analysis: Visualization, classification and +#' regression on subspaces and submanifolds. +#' Pattern Recognition. 2011 Jul 1;44(7):1357-71. \url{https://www.sciencedirect.com/science/article/pii/S0031320310005819?casa_token=AZMFg5OtPnAAAAAA:_Udu7GJ7G2ed1-XSmr-3IGSISUwcHfMpNtCj-qacXH5SBC4nwzVid36GXI3r8XG8dK5WOQui}; +#' @export +#' +#' @rdname RunSLSI +#' @export RunSLSI +#' +RunSLSI <- function(object, ...) { + UseMethod(generic = 'RunSLSI', object = object) +} + + + + #' Run Supervised Principal Component Analysis #' -#' Run a supervied PCA (SPCA) dimensionality reduction supervised by a cell-cell kernel. +#' Run a supervised PCA (SPCA) dimensionality reduction supervised by a cell-cell kernel. #' SPCA is used to capture a linear transformation which maximizes its dependency to #' the given cell-cell kernel. We use SNN graph as the kernel to supervise the linear #' matrix factorization. From 647344b1eaa4aa10b5d8c917ef11153cb079c49e Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Fri, 3 Dec 2021 14:02:14 -0500 Subject: [PATCH 24/53] Link to SeuratData repo --- vignettes/weighted_nearest_neighbor_analysis.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/weighted_nearest_neighbor_analysis.Rmd b/vignettes/weighted_nearest_neighbor_analysis.Rmd index 1116e3e95..4c207c7d0 100644 --- a/vignettes/weighted_nearest_neighbor_analysis.Rmd +++ b/vignettes/weighted_nearest_neighbor_analysis.Rmd @@ -40,7 +40,7 @@ We demonstrate the use of WNN analysis to two single-cell multimodal technologie # WNN analysis of CITE-seq, RNA + ADT We use the CITE-seq dataset from ([Stuart\*, Butler\* et al, Cell 2019](https://www.cell.com/cell/fulltext/S0092-8674(19)30559-8)), which consists of 30,672 scRNA-seq profiles measured alongside a panel of 25 antibodies from bone marrow. The object contains two assays, RNA and antibody-derived tags (ADT). -To run this vignette please install Seurat v4, available on [CRAN](https://cran.r-project.org/web/packages/Seurat/index.html). +To run this vignette please install Seurat v4, available on [CRAN](https://cran.r-project.org/web/packages/Seurat/index.html), and SeuratData, available on [GitHub](https://github.com/satijalab/seurat-data). ```{r install, eval = FALSE} install.packages("Seurat") From 7018f6b9869ee8e922a1a9bef184550405e2ed85 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Fri, 3 Dec 2021 15:21:30 -0500 Subject: [PATCH 25/53] Update docs --- man/FeaturePlot.Rd | 3 +++ 1 file changed, 3 insertions(+) diff --git a/man/FeaturePlot.Rd b/man/FeaturePlot.Rd index f869e4c98..9d334631c 100644 --- a/man/FeaturePlot.Rd +++ b/man/FeaturePlot.Rd @@ -25,6 +25,7 @@ FeaturePlot( blend.threshold = 0.5, label = FALSE, label.size = 4, + label.color = "black", repel = FALSE, ncol = NULL, coord.fixed = FALSE, @@ -94,6 +95,8 @@ different colors and different shapes on cells. Only applicable if \code{raster \item{label.size}{Sets size of labels} +\item{label.color}{Sets the color of the label text} + \item{repel}{Repel labels} \item{ncol}{Number of columns to combine multiple feature plots to, ignored if \code{split.by} is not \code{NULL}} From 3656475ddd087025e5aece4dbdb6be39622738a0 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Fri, 3 Dec 2021 15:22:59 -0500 Subject: [PATCH 26/53] Bump develop version Update changelog --- DESCRIPTION | 4 ++-- NEWS.md | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 187b5051e..d2bb0189a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Seurat -Version: 4.0.5.9003 -Date: 2021-10-22 +Version: 4.0.5.9004 +Date: 2021-12-03 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 4e0db768a..8a1df6b12 100644 --- a/NEWS.md +++ b/NEWS.md @@ -6,6 +6,7 @@ - Add `min.cells.group` parameter to `FindConservedMarkers` ([#5079](https://github.com/satijalab/seurat/pull/5079)) - Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors` - Fix error message in `ReadMtx()` ([#5158](https://github.com/satijalab/seurat/issues/5158)) +- Add `label.color` parameter to `FeaturePlot` ([#5314](https://github.com/satijalab/seurat/pull/5314)) # Seurat 4.0.5 (2020-10-04) ## Changes From 780d935ad2730d23d87e71e0d99adf46113add70 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Fri, 3 Dec 2021 16:46:11 -0500 Subject: [PATCH 27/53] Update required SeuratObject version --- DESCRIPTION | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 09e79dfbe..97e96e94c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -24,7 +24,6 @@ Authors@R: c( ) URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat BugReports: https://github.com/satijalab/seurat/issues -Remotes: mojaveazure/seurat-object@feat/export Depends: R (>= 4.0.0), methods @@ -67,7 +66,7 @@ Imports: scales, scattermore (>= 0.7), sctransform (>= 0.3.2), - SeuratObject (>= 4.0.2), + SeuratObject (>= 4.0.4), shiny, spatstat.core, spatstat.geom, From 24d51f844491b96f2c8ff09c6477fbf1d5987a53 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Fri, 3 Dec 2021 16:51:13 -0500 Subject: [PATCH 28/53] Adjust imports --- NAMESPACE | 5 ++++- R/integration.R | 2 ++ R/objects.R | 6 ++++++ R/preprocessing.R | 14 ++++++-------- R/utilities.R | 1 + 5 files changed, 19 insertions(+), 9 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 4e5c87530..bdc35dbcb 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -356,7 +356,6 @@ exportClasses(SeuratCommand) exportClasses(SpatialImage) exportClasses(TransferAnchorSet) exportClasses(VisiumV1) -import(Matrix) importClassesFrom(Matrix,dgCMatrix) importClassesFrom(SeuratObject,Assay) importClassesFrom(SeuratObject,DimReduc) @@ -369,6 +368,7 @@ importClassesFrom(SeuratObject,SpatialImage) importFrom(KernSmooth,bkde) importFrom(MASS,glm.nb) importFrom(MASS,lda) +importFrom(Matrix,Matrix) importFrom(Matrix,as.matrix) importFrom(Matrix,colMeans) importFrom(Matrix,colSums) @@ -378,6 +378,7 @@ importFrom(Matrix,rowMeans) importFrom(Matrix,rowSums) importFrom(Matrix,sparse.model.matrix) importFrom(Matrix,sparseMatrix) +importFrom(Matrix,t) importFrom(RANN,nn2) importFrom(RColorBrewer,brewer.pal) importFrom(RColorBrewer,brewer.pal.info) @@ -703,6 +704,7 @@ importFrom(utils,argsAnywhere) importFrom(utils,capture.output) importFrom(utils,file_test) importFrom(utils,globalVariables) +importFrom(utils,head) importFrom(utils,isS3method) importFrom(utils,isS3stdGeneric) importFrom(utils,methods) @@ -711,6 +713,7 @@ importFrom(utils,read.csv) importFrom(utils,read.delim) importFrom(utils,read.table) importFrom(utils,setTxtProgressBar) +importFrom(utils,tail) importFrom(utils,txtProgressBar) importFrom(utils,write.table) importFrom(uwot,umap) diff --git a/R/integration.R b/R/integration.R index 62150ed1b..bb4c37c5a 100644 --- a/R/integration.R +++ b/R/integration.R @@ -2615,6 +2615,8 @@ PrepSCTIntegration <- function( #' #' @return A vector of selected features #' +#' @importFrom utils head +#' #' @export #' @concept integration #' diff --git a/R/objects.R b/R/objects.R index e20b99b85..f772f8e33 100644 --- a/R/objects.R +++ b/R/objects.R @@ -2309,6 +2309,8 @@ setMethod( } ) +#' @importFrom utils head +# setMethod( f = 'show', signature = 'SCTAssay', @@ -2631,6 +2633,8 @@ SubsetVST <- function(sct.info, cells, features) { # @return The top \code{num} # @seealso \{code{\link{TopCells}}} \{code{\link{TopFeatures}}} # +#' @importFrom utils head tail +# Top <- function(data, num, balanced) { nr <- nrow(x = data) if (num > nr) { @@ -2833,6 +2837,8 @@ UpdateSlots <- function(object) { # @return Returns the data matrix if present (i.e.) not 0x0. Otherwise, returns an # appropriately sized empty sparse matrix # +#' @importFrom Matrix Matrix +# ValidateDataForMerge <- function(assay, slot) { mat <- GetAssayData(object = assay, slot = slot) if (any(dim(x = mat) == c(0, 0))) { diff --git a/R/preprocessing.R b/R/preprocessing.R index 6e9363c41..f04537494 100644 --- a/R/preprocessing.R +++ b/R/preprocessing.R @@ -606,7 +606,6 @@ LoadSTARmap <- function( #' #' @return Returns a matrix with the normalize and log transformed data #' -#' @import Matrix #' @importFrom methods as #' #' @export @@ -649,8 +648,6 @@ LogNormalize <- function(data, scale.factor = 1e4, verbose = TRUE) { #' #' @return A Seurat object with demultiplexing results stored at \code{object$MULTI_ID} #' -#' @import Matrix -#' #' @export #' @concept preprocessing #' @@ -1284,8 +1281,8 @@ ReadSlideSeq <- function(coord.file, assay = 'Spatial') { #' @param verbose Print progress #' @return Returns a matrix with the relative counts #' -#' @import Matrix #' @importFrom methods as +#' @importFrom Matrix colSums #' #' @export #' @concept preprocessing @@ -1307,7 +1304,7 @@ RelativeCounts <- function(data, scale.factor = 1, verbose = TRUE) { cat("Performing relative-counts-normalization\n", file = stderr()) } norm.data <- data - norm.data@x <- norm.data@x / rep.int(colSums(norm.data), diff(norm.data@p)) * scale.factor + norm.data@x <- norm.data@x / rep.int(Matrix::colSums(norm.data), diff(norm.data@p)) * scale.factor return(norm.data) } @@ -1432,7 +1429,6 @@ RunMoransI <- function(data, pos, verbose = TRUE) { #' @param upsample Upsamples all cells with fewer than max.umi #' @param verbose Display the progress bar #' -#' @import Matrix #' @importFrom methods as #' #' @return Matrix with downsampled data @@ -2008,6 +2004,8 @@ FindVariableFeatures.default <- function( #' #' @rdname FindVariableFeatures #' @concept preprocessing +#' +#' @importFrom utils head #' @export #' @method FindVariableFeatures Assay #' @@ -3091,9 +3089,9 @@ ComputeRMetric <- function(mv, r.metric = 5) { # # @return Returns a matrix with the custom normalization # +#' @importFrom Matrix t #' @importFrom methods as #' @importFrom pbapply pbapply -# @import Matrix # CustomNormalize <- function(data, custom_function, margin, verbose = TRUE) { if (is.data.frame(x = data)) { @@ -3117,7 +3115,7 @@ CustomNormalize <- function(data, custom_function, margin, verbose = TRUE) { MARGIN = margin, FUN = custom_function) if (margin == 1) { - norm.data = t(x = norm.data) + norm.data = Matrix::t(x = norm.data) } colnames(x = norm.data) <- colnames(x = data) rownames(x = norm.data) <- rownames(x = data) diff --git a/R/utilities.R b/R/utilities.R index c5710b6be..ac0ed0985 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -581,6 +581,7 @@ CellCycleScoring <- function( #' \code{ncontrols} most highly expressed features are kept, and the #' prefix is kept. All other rows are retained. #' +#' @importFrom utils head #' @importFrom Matrix rowSums #' #' @export From 07ae97c344a9b18001defe4fd2db0e545bf22cf0 Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Fri, 3 Dec 2021 18:19:22 -0500 Subject: [PATCH 29/53] remove extra line --- R/utilities.R | 2 -- 1 file changed, 2 deletions(-) diff --git a/R/utilities.R b/R/utilities.R index ac0ed0985..70cf29b50 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -1092,8 +1092,6 @@ MinMax <- function(data, min, max) { #' #' @export #' -#' @export -#' #' @examples #' set.seed(42) #' PercentAbove(sample(1:100, 10), 75) From 42a802309c96cfc56fea7f1534bb46c597af672b Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Fri, 3 Dec 2021 18:24:36 -0500 Subject: [PATCH 30/53] Add concepts to new docs --- R/utilities.R | 104 +++++++++++++++++++++++++++++-------------- R/visualization.R | 35 +-------------- man/AutoPointSize.Rd | 1 + man/PercentAbove.Rd | 1 + man/SetQuantile.Rd | 3 +- 5 files changed, 75 insertions(+), 69 deletions(-) diff --git a/R/utilities.R b/R/utilities.R index ac0ed0985..f77694624 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -985,6 +985,27 @@ GroupCorrelation <- function( return(object) } +#' Load the Annoy index file +#' +#' @param object Neighbor object +#' @param file Path to file with annoy index +#' +#' @return Returns the Neighbor object with the index stored +#' @export +#' @concept utilities +#' +LoadAnnoyIndex <- function(object, file){ + metric <- slot(object = object, name = "alg.info")$metric + ndim <- slot(object = object, name = "alg.info")$ndim + if (is.null(x = metric)) { + stop("Provided Neighbor object wasn't generated with annoy") + } + annoy.idx <- CreateAnn(name = metric, ndim = ndim) + annoy.idx$load(path.expand(path = file)) + Index(object = object) <- annoy.idx + return(object) +} + #' Calculate the variance to mean ratio of logged values #' #' Calculate the variance to mean ratio (VMR) in non-logspace (return answer in @@ -1093,6 +1114,7 @@ MinMax <- function(data, min, max) { #' @export #' #' @export +#' @concept utilities #' #' @examples #' set.seed(42) @@ -1433,24 +1455,34 @@ PseudobulkExpression <- function( } } -#' Load the Annoy index file +#' Regroup idents based on meta.data info #' -#' @param object Neighbor object -#' @param file Path to file with annoy index +#' For cells in each ident, set a new identity based on the most common value +#' of a specified metadata column. +#' +#' @param object Seurat object +#' @param metadata Name of metadata column +#' @return A Seurat object with the active idents regrouped #' -#' @return Returns the Neighbor object with the index stored #' @export #' @concept utilities #' -LoadAnnoyIndex <- function(object, file){ - metric <- slot(object = object, name = "alg.info")$metric - ndim <- slot(object = object, name = "alg.info")$ndim - if (is.null(x = metric)) { - stop("Provided Neighbor object wasn't generated with annoy") +#' @examples +#' data("pbmc_small") +#' pbmc_small <- RegroupIdents(pbmc_small, metadata = "groups") +#' +RegroupIdents <- function(object, metadata) { + for (ii in levels(x = object)) { + ident.cells <- WhichCells(object = object, idents = ii) + if (length(x = ident.cells) == 0) { + next + } + new.ident <- names(x = which.max(x = table(object[[metadata]][ident.cells, ]))) + if (is.null(x = new.ident)) { + stop("Cluster ", ii, " contains only cells with NA values in the '", metadata, "' metadata column.") + } + Idents(object = object, cells = ident.cells) <- new.ident } - annoy.idx <- CreateAnn(name = metric, ndim = ndim) - annoy.idx$load(path.expand(path = file)) - Index(object = object) <- annoy.idx return(object) } @@ -1473,35 +1505,39 @@ SaveAnnoyIndex <- function( index$save(path.expand(path = file)) } -#' Regroup idents based on meta.data info +#' Find the Quantile of Data #' -#' For cells in each ident, set a new identity based on the most common value -#' of a specified metadata column. +#' Converts a quantile in character form to a number regarding some data. +#' String form for a quantile is represented as a number prefixed with +#' \dQuote{q}; for example, 10th quantile is \dQuote{q10} while 2nd quantile is +#' \dQuote{q2}. Will only take a quantile of non-zero data values #' -#' @param object Seurat object -#' @param metadata Name of metadata column -#' @return A Seurat object with the active idents regrouped +#' @param cutoff The cutoff to turn into a quantile +#' @param data The data to turn find the quantile of +#' +#' @return The numerical representation of the quantile +#' +#' @importFrom stats quantile #' #' @export #' @concept utilities #' #' @examples -#' data("pbmc_small") -#' pbmc_small <- RegroupIdents(pbmc_small, metadata = "groups") -#' -RegroupIdents <- function(object, metadata) { - for (ii in levels(x = object)) { - ident.cells <- WhichCells(object = object, idents = ii) - if (length(x = ident.cells) == 0) { - next - } - new.ident <- names(x = which.max(x = table(object[[metadata]][ident.cells, ]))) - if (is.null(x = new.ident)) { - stop("Cluster ", ii, " contains only cells with NA values in the '", metadata, "' metadata column.") - } - Idents(object = object, cells = ident.cells) <- new.ident - } - return(object) +#' set.seed(42) +#' SetQuantile('q10', sample(1:100, 10)) +#' +SetQuantile <- function(cutoff, data) { + if (grepl(pattern = '^q[0-9]{1,2}$', x = as.character(x = cutoff), perl = TRUE)) { + this.quantile <- as.numeric(x = sub( + pattern = 'q', + replacement = '', + x = as.character(x = cutoff) + )) / 100 + data <- unlist(x = data) + data <- data[data > 0] + cutoff <- quantile(x = data, probs = this.quantile) + } + return(as.numeric(x = cutoff)) } #' @rdname UpdateSymbolList diff --git a/R/visualization.R b/R/visualization.R index 8e657cb75..067af9fb2 100644 --- a/R/visualization.R +++ b/R/visualization.R @@ -4015,6 +4015,7 @@ AugmentPlot <- function(plot, width = 10, height = 10, dpi = 100) { #' @return The "optimal" point size for visualizing these data #' #' @export +#' @concept visualization #' #' @examples #' df <- data.frame(x = rnorm(n = 10000), y = runif(n = 10000)) @@ -4942,40 +4943,6 @@ PurpleAndYellow <- function(k = 50) { return(CustomPalette(low = "magenta", high = "yellow", mid = "black", k = k)) } -#' Find the Quantile of Data -#' -#' Converts a quantile in character form to a number regarding some data. -#' String form for a quantile is represented as a number prefixed with -#' \dQuote{q}; for example, 10th quantile is \dQuote{q10} while 2nd quantile is -#' \dQuote{q2}. Will only take a quantile of non-zero data values -#' -#' @param cutoff The cutoff to turn into a quantile -#' @param data The data to turn find the quantile of -#' -#' @return The numerical representation of the quantile -#' -#' @importFrom stats quantile -#' -#' @export -#' -#' @examples -#' set.seed(42) -#' SetQuantile('q10', sample(1:100, 10)) -#' -SetQuantile <- function(cutoff, data) { - if (grepl(pattern = '^q[0-9]{1,2}$', x = as.character(x = cutoff), perl = TRUE)) { - this.quantile <- as.numeric(x = sub( - pattern = 'q', - replacement = '', - x = as.character(x = cutoff) - )) / 100 - data <- unlist(x = data) - data <- data[data > 0] - cutoff <- quantile(x = data, probs = this.quantile) - } - return(as.numeric(x = cutoff)) -} - #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% # Seurat themes #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% diff --git a/man/AutoPointSize.Rd b/man/AutoPointSize.Rd index 362239b04..7e908dda1 100644 --- a/man/AutoPointSize.Rd +++ b/man/AutoPointSize.Rd @@ -22,3 +22,4 @@ df <- data.frame(x = rnorm(n = 10000), y = runif(n = 10000)) AutoPointSize(data = df) } +\concept{visualization} diff --git a/man/PercentAbove.Rd b/man/PercentAbove.Rd index 403dbfe2b..646e77670 100644 --- a/man/PercentAbove.Rd +++ b/man/PercentAbove.Rd @@ -22,3 +22,4 @@ set.seed(42) PercentAbove(sample(1:100, 10), 75) } +\concept{utilities} diff --git a/man/SetQuantile.Rd b/man/SetQuantile.Rd index 598a2f6c3..3b4980029 100644 --- a/man/SetQuantile.Rd +++ b/man/SetQuantile.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/visualization.R +% Please edit documentation in R/utilities.R \name{SetQuantile} \alias{SetQuantile} \title{Find the Quantile of Data} @@ -25,3 +25,4 @@ set.seed(42) SetQuantile('q10', sample(1:100, 10)) } +\concept{utilities} From bbba8dc112deb5d2fa177168b6d8b54b65195b29 Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Sun, 5 Dec 2021 13:20:38 -0500 Subject: [PATCH 31/53] Clean up code and documentation --- R/dimensional_reduction.R | 74 ++++++++++++++++++--------------------- 1 file changed, 34 insertions(+), 40 deletions(-) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 2f7589f19..0a3abeb57 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -2260,12 +2260,12 @@ L2Norm <- function(vec) { # @param features Features to use as input for the dimensional reduction technique. # Default is variable features # @ param verbose Print messages and warnings -# @importFrom sparseMatrixStats rowVars +#' @importFrom sparseMatrixStats rowVars # PrepDR <- function( object, features = NULL, - slot = 'scale.data', + slot = 'scale.data', verbose = TRUE ) { if (length(x = VariableFeatures(object = object)) == 0 && is.null(x = features)) { @@ -2284,7 +2284,7 @@ PrepDR <- function( } } features <- features.keep - + if (inherits(x = data.use, what = 'dgCMatrix')) { features.var <- rowVars(x = data.use[features, ]) } @@ -2433,18 +2433,17 @@ RunSPCA.Seurat <- function( return(object) } - #' @param assay Name of Assay SLSI is being run on -#' @param npcs Total Number of SLSIs to compute and store (50 by default) -#' @param verbose Print the top genes associated with high/low loadings for -#' the SLSIs +#' @param n Total Number of SLSI components to compute and store +#' @param verbose Display messages #' @param reduction.key dimensional reduction key, specifies the string before -#' the number for the dimension names. SLSI by default +#' the number for the dimension names #' @param graph Graph used supervised by SLSI -#' @param seed.use Set a random seed. By default, sets the seed to 42. Setting -#' NULL will not set a seed. +#' @param project Project cell embeddings using SLSI feature loadings +#' @param seed.use Set a random seed. Setting NULL will not set a seed. #' #' @importFrom irlba irlba +#' @importMethodsFrom Matrix t #' #' @concept dimensional_reduction #' @rdname RunSLSI @@ -2452,70 +2451,68 @@ RunSPCA.Seurat <- function( RunSLSI.default <- function( object, assay = NULL, - nlsi = 50, + n = 50, reduction.key = "SLSI_", graph = NULL, verbose = TRUE, - project = TRUE, + project = TRUE, seed.use = 42, ... ) { if (!is.null(x = seed.use)) { set.seed(seed = seed.use) } - nlsi <- min(nlsi, nrow(x = object) - 1) - + n <- min(n, nrow(x = object) - 1) + if (verbose) { message("Smoothing peaks matrix") } - object.smooth <- t(graph) %*% (t(object) %*% object) %*% graph + object.smooth <- t(x = graph) %*% (t(x = object) %*% object) %*% graph if (verbose) { message("Performing eigendecomposition") } - svd.V <- irlba(A = object.smooth, nv = nlsi, nu = nlsi) - sigma <- sqrt(x = svd.V$d) + svd.V <- irlba(A = object.smooth, nv = n, nu = n) + sigma <- sqrt(x = svd.V$d) feature.loadings <- object %*% (graph %*% svd.V$u) %*% diag(x = 1/sigma) feature.loadings <- as.matrix(x = feature.loadings) if (project) { - cell.embeddings <- t(object) %*% feature.loadings %*% diag(x = 1/sigma) + cell.embeddings <- t(x = object) %*% feature.loadings %*% diag(x = 1/sigma) } else { cell.embeddings <- svd.V$u - rownames(cell.embeddings) <- colnames(object) + rownames(x = cell.embeddings) <- colnames(x = object) } cell.embeddings <- as.matrix(x = cell.embeddings) - + # construct svd list stored in misc for LSI projection svd.lsi <- svd.V svd.lsi$d <- sigma svd.lsi$u <- feature.loadings svd.lsi$v <- cell.embeddings - + colnames(x = cell.embeddings) <- paste0(reduction.key, 1:ncol(cell.embeddings)) - reduction.data <- CreateDimReducObject(embeddings = cell.embeddings, - loadings = feature.loadings, - key = reduction.key, - assay = assay, - misc = svd.lsi + reduction.data <- CreateDimReducObject( + embeddings = cell.embeddings, + loadings = feature.loadings, + key = reduction.key, + assay = assay, + misc = svd.lsi ) return(reduction.data) } - - - -#' @param features Features to compute SLSI on. If features=NULL, SLSI will be run +#' @param features Features to compute SLSI on. If NULL, SLSI will be run #' using the variable features for the Assay. #' #' @rdname RunSLSI #' @concept dimensional_reduction #' @export -#' @method RunSPCA Assay +#' @method RunSLSI Assay #' RunSLSI.Assay <- function( object, assay = NULL, features = NULL, - nlsi = 50, + n = 50, reduction.key = "SLSI_", graph = NULL, verbose = TRUE, @@ -2525,13 +2522,13 @@ RunSLSI.Assay <- function( data.use <- PrepDR( object = object, features = features, - slot = "data", + slot = "data", verbose = verbose ) reduction.data <- RunSLSI( object = data.use, assay = assay, - nlsi = nlsi, + n = n, reduction.key = reduction.key, graph = graph, verbose = verbose, @@ -2541,10 +2538,7 @@ RunSLSI.Assay <- function( return(reduction.data) } - - - -#' @param reduction.name dimensional reduction name, spca by default +#' @param reduction.name dimensional reduction name #' @rdname RunSLSI #' @concept dimensional_reduction #' @export @@ -2554,7 +2548,7 @@ RunSLSI.Seurat <- function( object, assay = NULL, features = NULL, - nlsi = 50, + n = 50, reduction.name = "slsi", reduction.key = "SLSI_", graph = NULL, @@ -2573,7 +2567,7 @@ RunSLSI.Seurat <- function( object = assay.data, assay = assay, features = features, - nlsi = nlsi, + n = n, reduction.name = reduction.name, reduction.key = reduction.key, graph = graph, From 7ccd4c93894387dcaedb6855285c4467595a80b5 Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Sun, 5 Dec 2021 13:21:13 -0500 Subject: [PATCH 32/53] Update docs --- NAMESPACE | 3 +- man/RunSLSI.Rd | 89 ++++++++++++++++++++++++++++++++++++++++++++++++++ man/RunSPCA.Rd | 2 +- 3 files changed, 92 insertions(+), 2 deletions(-) create mode 100644 man/RunSLSI.Rd diff --git a/NAMESPACE b/NAMESPACE index 5c3ca7270..009f4728c 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -442,7 +442,6 @@ importFrom(SeuratObject,as.Graph) importFrom(SeuratObject,as.Neighbor) importFrom(SeuratObject,as.Seurat) importFrom(SeuratObject,as.sparse) -importFrom(sparseMatrixStats, rowVars) importFrom(cluster,clara) importFrom(cowplot,get_legend) importFrom(cowplot,plot_grid) @@ -651,6 +650,7 @@ importFrom(shiny,sliderInput) importFrom(shiny,stopApp) importFrom(shiny,updateSelectInput) importFrom(shiny,verbatimTextOutput) +importFrom(sparseMatrixStats,rowVars) importFrom(spatstat.core,markvario) importFrom(spatstat.geom,ppp) importFrom(stats,aggregate) @@ -707,4 +707,5 @@ importFrom(utils,txtProgressBar) importFrom(utils,write.table) importFrom(uwot,umap) importFrom(uwot,umap_transform) +importMethodsFrom(Matrix,t) useDynLib(Seurat) diff --git a/man/RunSLSI.Rd b/man/RunSLSI.Rd new file mode 100644 index 000000000..ae0bef90d --- /dev/null +++ b/man/RunSLSI.Rd @@ -0,0 +1,89 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/generics.R, R/dimensional_reduction.R +\name{RunSLSI} +\alias{RunSLSI} +\alias{RunSLSI.default} +\alias{RunSLSI.Assay} +\alias{RunSLSI.Seurat} +\title{Run Supervised Latent Semantic Indexing} +\usage{ +RunSLSI(object, ...) + +\method{RunSLSI}{default}( + object, + assay = NULL, + n = 50, + reduction.key = "SLSI_", + graph = NULL, + verbose = TRUE, + project = TRUE, + seed.use = 42, + ... +) + +\method{RunSLSI}{Assay}( + object, + assay = NULL, + features = NULL, + n = 50, + reduction.key = "SLSI_", + graph = NULL, + verbose = TRUE, + seed.use = 42, + ... +) + +\method{RunSLSI}{Seurat}( + object, + assay = NULL, + features = NULL, + n = 50, + reduction.name = "slsi", + reduction.key = "SLSI_", + graph = NULL, + verbose = TRUE, + seed.use = 42, + ... +) +} +\arguments{ +\item{object}{An object} + +\item{...}{Arguments passed to other methods} + +\item{assay}{Name of Assay SLSI is being run on} + +\item{n}{Total Number of SLSI components to compute and store} + +\item{reduction.key}{dimensional reduction key, specifies the string before +the number for the dimension names} + +\item{graph}{Graph used supervised by SLSI} + +\item{verbose}{Display messages} + +\item{project}{Project cell embeddings using SLSI feature loadings} + +\item{seed.use}{Set a random seed. Setting NULL will not set a seed.} + +\item{features}{Features to compute SLSI on. If NULL, SLSI will be run +using the variable features for the Assay.} + +\item{reduction.name}{dimensional reduction name} +} +\value{ +Returns Seurat object with the SPCA calculation stored in the +reductions slot +} +\description{ +Run a supervised LSI (SLSI) dimensionality reduction supervised by a +cell-cell kernel. SLSI is used to capture a linear transformation that +maximizes its dependency to the given cell-cell kernel. +} +\references{ +Barshan E, Ghodsi A, Azimifar Z, Jahromi MZ. +Supervised principal component analysis: Visualization, classification and +regression on subspaces and submanifolds. +Pattern Recognition. 2011 Jul 1;44(7):1357-71. \url{https://www.sciencedirect.com/science/article/pii/S0031320310005819?casa_token=AZMFg5OtPnAAAAAA:_Udu7GJ7G2ed1-XSmr-3IGSISUwcHfMpNtCj-qacXH5SBC4nwzVid36GXI3r8XG8dK5WOQui}; +} +\concept{dimensional_reduction} diff --git a/man/RunSPCA.Rd b/man/RunSPCA.Rd index 8c05b3839..fb166c30c 100644 --- a/man/RunSPCA.Rd +++ b/man/RunSPCA.Rd @@ -74,7 +74,7 @@ using the variable features for the Assay.} Returns Seurat object with the SPCA calculation stored in the reductions slot } \description{ -Run a supervied PCA (SPCA) dimensionality reduction supervised by a cell-cell kernel. +Run a supervised PCA (SPCA) dimensionality reduction supervised by a cell-cell kernel. SPCA is used to capture a linear transformation which maximizes its dependency to the given cell-cell kernel. We use SNN graph as the kernel to supervise the linear matrix factorization. From e4d45393ced0dccff6b75dc3808b93268b483f8a Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Sun, 5 Dec 2021 13:21:30 -0500 Subject: [PATCH 33/53] Update SLSI generic --- R/generics.R | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/R/generics.R b/R/generics.R index e8d04e955..09ced91f8 100644 --- a/R/generics.R +++ b/R/generics.R @@ -441,18 +441,17 @@ RunPCA <- function(object, ...) { UseMethod(generic = 'RunPCA', object = object) } - - #' Run Supervised Latent Semantic Indexing #' -#' Run a supervised LSI (SLSI) dimensionality reduction supervised by a cell-cell kernel. -#' SLSI is used to capture a linear transformation which maximizes its dependency to -#' the given cell-cell kernel. +#' Run a supervised LSI (SLSI) dimensionality reduction supervised by a +#' cell-cell kernel. SLSI is used to capture a linear transformation that +#' maximizes its dependency to the given cell-cell kernel. #' #' @param object An object -#' @param ... Arguments passed to other methods and IRLBA +#' @param ... Arguments passed to other methods #' -#' @return Returns Seurat object with the SPCA calculation stored in the reductions slot +#' @return Returns Seurat object with the SPCA calculation stored in the +#' reductions slot #' @references Barshan E, Ghodsi A, Azimifar Z, Jahromi MZ. #' Supervised principal component analysis: Visualization, classification and #' regression on subspaces and submanifolds. @@ -466,9 +465,6 @@ RunSLSI <- function(object, ...) { UseMethod(generic = 'RunSLSI', object = object) } - - - #' Run Supervised Principal Component Analysis #' #' Run a supervised PCA (SPCA) dimensionality reduction supervised by a cell-cell kernel. From d81e5b28ea286b42a5344dbd98d0a6a866c3bf48 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Mon, 6 Dec 2021 12:50:47 -0500 Subject: [PATCH 34/53] remove project parameter --- R/dimensional_reduction.R | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 0a3abeb57..1a80085d4 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -2439,7 +2439,6 @@ RunSPCA.Seurat <- function( #' @param reduction.key dimensional reduction key, specifies the string before #' the number for the dimension names #' @param graph Graph used supervised by SLSI -#' @param project Project cell embeddings using SLSI feature loadings #' @param seed.use Set a random seed. Setting NULL will not set a seed. #' #' @importFrom irlba irlba @@ -2455,7 +2454,6 @@ RunSLSI.default <- function( reduction.key = "SLSI_", graph = NULL, verbose = TRUE, - project = TRUE, seed.use = 42, ... ) { @@ -2475,12 +2473,7 @@ RunSLSI.default <- function( sigma <- sqrt(x = svd.V$d) feature.loadings <- object %*% (graph %*% svd.V$u) %*% diag(x = 1/sigma) feature.loadings <- as.matrix(x = feature.loadings) - if (project) { - cell.embeddings <- t(x = object) %*% feature.loadings %*% diag(x = 1/sigma) - } else { - cell.embeddings <- svd.V$u - rownames(x = cell.embeddings) <- colnames(x = object) - } + cell.embeddings <- t(x = object) %*% feature.loadings %*% diag(x = 1/sigma) cell.embeddings <- as.matrix(x = cell.embeddings) # construct svd list stored in misc for LSI projection From 8e7e610f069bb72dd3c29ceffb5e6d091bf77b14 Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Tue, 7 Dec 2021 11:27:33 -0500 Subject: [PATCH 35/53] Update docs --- man/RunSLSI.Rd | 3 --- 1 file changed, 3 deletions(-) diff --git a/man/RunSLSI.Rd b/man/RunSLSI.Rd index ae0bef90d..05f716857 100644 --- a/man/RunSLSI.Rd +++ b/man/RunSLSI.Rd @@ -16,7 +16,6 @@ RunSLSI(object, ...) reduction.key = "SLSI_", graph = NULL, verbose = TRUE, - project = TRUE, seed.use = 42, ... ) @@ -62,8 +61,6 @@ the number for the dimension names} \item{verbose}{Display messages} -\item{project}{Project cell embeddings using SLSI feature loadings} - \item{seed.use}{Set a random seed. Setting NULL will not set a seed.} \item{features}{Features to compute SLSI on. If NULL, SLSI will be run From 8ebb179fe04747d72ac0a7a850d04e0b0d9feb31 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Fri, 10 Dec 2021 13:04:07 -0500 Subject: [PATCH 36/53] add row operations from avi --- R/RcppExports.R | 12 ++++++++++++ src/RcppExports.cpp | 45 +++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) diff --git a/R/RcppExports.R b/R/RcppExports.R index dc597cc64..bf0f9e645 100644 --- a/R/RcppExports.R +++ b/R/RcppExports.R @@ -109,3 +109,15 @@ SNN_SmallestNonzero_Dist <- function(snn, mat, n, nearest_dist) { .Call('_Seurat_SNN_SmallestNonzero_Dist', PACKAGE = 'Seurat', snn, mat, n, nearest_dist) } +row_sum_dgcmatrix <- function(x, i, rows, cols) { + .Call('_Seurat_row_sum_dgcmatrix', PACKAGE = 'Seurat', x, i, rows, cols) +} + +row_mean_dgcmatrix <- function(x, i, rows, cols) { + .Call('_Seurat_row_mean_dgcmatrix', PACKAGE = 'Seurat', x, i, rows, cols) +} + +row_var_dgcmatrix <- function(x, i, rows, cols) { + .Call('_Seurat_row_var_dgcmatrix', PACKAGE = 'Seurat', x, i, rows, cols) +} + diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index 7ec3c42e2..7a3302c6b 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -359,6 +359,48 @@ BEGIN_RCPP return rcpp_result_gen; END_RCPP } +// row_sum_dgcmatrix +NumericVector row_sum_dgcmatrix(NumericVector& x, IntegerVector& i, int rows, int cols); +RcppExport SEXP _Seurat_row_sum_dgcmatrix(SEXP xSEXP, SEXP iSEXP, SEXP rowsSEXP, SEXP colsSEXP) { +BEGIN_RCPP + Rcpp::RObject rcpp_result_gen; + Rcpp::RNGScope rcpp_rngScope_gen; + Rcpp::traits::input_parameter< NumericVector& >::type x(xSEXP); + Rcpp::traits::input_parameter< IntegerVector& >::type i(iSEXP); + Rcpp::traits::input_parameter< int >::type rows(rowsSEXP); + Rcpp::traits::input_parameter< int >::type cols(colsSEXP); + rcpp_result_gen = Rcpp::wrap(row_sum_dgcmatrix(x, i, rows, cols)); + return rcpp_result_gen; +END_RCPP +} +// row_mean_dgcmatrix +NumericVector row_mean_dgcmatrix(NumericVector& x, IntegerVector& i, int rows, int cols); +RcppExport SEXP _Seurat_row_mean_dgcmatrix(SEXP xSEXP, SEXP iSEXP, SEXP rowsSEXP, SEXP colsSEXP) { +BEGIN_RCPP + Rcpp::RObject rcpp_result_gen; + Rcpp::RNGScope rcpp_rngScope_gen; + Rcpp::traits::input_parameter< NumericVector& >::type x(xSEXP); + Rcpp::traits::input_parameter< IntegerVector& >::type i(iSEXP); + Rcpp::traits::input_parameter< int >::type rows(rowsSEXP); + Rcpp::traits::input_parameter< int >::type cols(colsSEXP); + rcpp_result_gen = Rcpp::wrap(row_mean_dgcmatrix(x, i, rows, cols)); + return rcpp_result_gen; +END_RCPP +} +// row_var_dgcmatrix +NumericVector row_var_dgcmatrix(NumericVector& x, IntegerVector& i, int rows, int cols); +RcppExport SEXP _Seurat_row_var_dgcmatrix(SEXP xSEXP, SEXP iSEXP, SEXP rowsSEXP, SEXP colsSEXP) { +BEGIN_RCPP + Rcpp::RObject rcpp_result_gen; + Rcpp::RNGScope rcpp_rngScope_gen; + Rcpp::traits::input_parameter< NumericVector& >::type x(xSEXP); + Rcpp::traits::input_parameter< IntegerVector& >::type i(iSEXP); + Rcpp::traits::input_parameter< int >::type rows(rowsSEXP); + Rcpp::traits::input_parameter< int >::type cols(colsSEXP); + rcpp_result_gen = Rcpp::wrap(row_var_dgcmatrix(x, i, rows, cols)); + return rcpp_result_gen; +END_RCPP +} RcppExport SEXP isnull(SEXP); @@ -390,6 +432,9 @@ static const R_CallMethodDef CallEntries[] = { {"_Seurat_WriteEdgeFile", (DL_FUNC) &_Seurat_WriteEdgeFile, 3}, {"_Seurat_DirectSNNToFile", (DL_FUNC) &_Seurat_DirectSNNToFile, 4}, {"_Seurat_SNN_SmallestNonzero_Dist", (DL_FUNC) &_Seurat_SNN_SmallestNonzero_Dist, 4}, + {"_Seurat_row_sum_dgcmatrix", (DL_FUNC) &_Seurat_row_sum_dgcmatrix, 4}, + {"_Seurat_row_mean_dgcmatrix", (DL_FUNC) &_Seurat_row_mean_dgcmatrix, 4}, + {"_Seurat_row_var_dgcmatrix", (DL_FUNC) &_Seurat_row_var_dgcmatrix, 4}, {"isnull", (DL_FUNC) &isnull, 1}, {NULL, NULL, 0} }; From c50ff021ef53d2e774fb02dc027c40c01fca70a5 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Fri, 10 Dec 2021 13:05:35 -0500 Subject: [PATCH 37/53] add c++ functions --- src/stats.cpp | 41 +++++++++++++++++++++++++++++++++++++++++ src/stats.o | Bin 0 -> 435256 bytes 2 files changed, 41 insertions(+) create mode 100644 src/stats.cpp create mode 100644 src/stats.o diff --git a/src/stats.cpp b/src/stats.cpp new file mode 100644 index 000000000..4b7f18591 --- /dev/null +++ b/src/stats.cpp @@ -0,0 +1,41 @@ +#include + +using namespace Rcpp; + +// [[Rcpp::export]] +NumericVector row_sum_dgcmatrix(NumericVector &x, IntegerVector &i, int rows, int cols) { + NumericVector rowsum(rows, 0.0); + int x_length = x.length(); + for (int k=0; kw*}mFhq-eZz!^nykf;PD3^@r110#}^AUPulh$Iy;AVJ0v#f+Fh1VJ%j z!hiw>Fk{Ayii+ZA00Tz;z0awxu6yV5`K|ZAxBmC9^=7T^I$e98Q>Us@gE6Oo=_;7{=`<^!g><@=&qg}K$}?>`%cirD&cShxy*}5b=h<{F((`f5v)32c^g^3n zg!Ez@^X>Hln=Z8JBBYD0d@0f;RxU((8IB?xm)pFhNUyN+l}MN2xC+PBHt!mw*IM~H zq}N;d2AeKNdZU$B*z_i(H(U7@q_KtbUbrxwirb~)sN!p&#=edti(!{cxs zS5Q=qxXn;X4I|nq5$|h-M0wUPq0B2v}yR 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ze~&r7RsUUF|2Th-x$<=XKk|4x{&QHrnVf)4*Z;d7{XK^MGxrhx!K${nOli z9;^Q^W@5Sif3=5S$NcN5(qPl|_eYLzwcj%Ke~`IUe?M`@y8rx(NB?2gzYetNQ0qVG z(H}ANe`@HjclTMW`l~)I6n4eW*~k{RKlbp`%&$gccdY#{IKEYXl^+k=AIJZ=^Z`J>lQUA{v z`WJfi`&oaD_0SffYd!o*zHz<^joq>K|9R%?@1L5O-=z3b{{l}s zzSV!axc!FNklOE;?pXLTubk}G+2oVfA7T9@^JOP|`FysV_p)2wg-f)f_gScl^!MLQtk26Rk(>EFssI-;U$#4PpP0aZdgJ zXv6=_?7yNXDw84d5A=W?Y;!*)5})?yr&zz~-$MrJ)9=5Au)>o4hZb{6Eh9)BfM$(SM#E45ZC{KaQK$zrmxQ z_*kev&Ivr}pJ3?U(390|8r#$6X%EiOFtw3-|zkjU-0KV{!g;L zzJDiv%l<{?i+{2|<`;TIhi8N*b_sWZAxycSs9^rIyT6Z{_%GORC4K>TKgIE<-1jTA zQT!it|Aa5`TiRs5;JMKMrjOF6L}HOMe97%KpNh94Z9O`ie>!*`q%vqDJ>1;#)#N8H N4BPJ{bph7={|9R?aJc{g literal 0 HcmV?d00001 From db95fd7270f8877f9b04f14cda439324932338f8 Mon Sep 17 00:00:00 2001 From: Avi Srivastava Date: Fri, 10 Dec 2021 14:26:42 -0500 Subject: [PATCH 38/53] Update stats.cpp --- src/stats.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/stats.cpp b/src/stats.cpp index 4b7f18591..76d1ca8a4 100644 --- a/src/stats.cpp +++ b/src/stats.cpp @@ -2,6 +2,7 @@ using namespace Rcpp; +// the following code in-parts taken from sparseMatrixStats (http://www.bioconductor.org/packages/release/bioc/html/sparseMatrixStats.html). // [[Rcpp::export]] NumericVector row_sum_dgcmatrix(NumericVector &x, IntegerVector &i, int rows, int cols) { NumericVector rowsum(rows, 0.0); @@ -38,4 +39,4 @@ NumericVector row_var_dgcmatrix(NumericVector &x, IntegerVector &i, int rows, in rowvar[k] = (rowvar[k] + (pow(rowmean[k], 2) * nzero[k])) / (cols - 1); } return rowvar; -} \ No newline at end of file +} From a3ea4756203fd5fd120e0262910b66f37373bf75 Mon Sep 17 00:00:00 2001 From: timoast <4591688+timoast@users.noreply.github.com> Date: Fri, 10 Dec 2021 14:29:24 -0500 Subject: [PATCH 39/53] Update license --- .Rbuildignore | 1 + DESCRIPTION | 2 +- LICENSE | 676 +------------------------------------------------- LICENSE.md | 21 ++ 4 files changed, 25 insertions(+), 675 deletions(-) create mode 100644 LICENSE.md diff --git a/.Rbuildignore b/.Rbuildignore index bfb0f62ca..7442342ca 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -13,3 +13,4 @@ CODE_OF_CONDUCT.md ^pkgdown$ ^index\.md$ ^vignettes$ +^LICENSE\.md$ diff --git a/DESCRIPTION b/DESCRIPTION index 6b8fdfc9f..d474755cb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -76,7 +76,7 @@ Imports: utils, uwot (>= 0.1.9) LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress -License: GPL-3 | file LICENSE +License: MIT + file LICENSE LazyData: true Collate: 'RcppExports.R' diff --git a/LICENSE b/LICENSE index 9cecc1d46..95c337c65 100644 --- a/LICENSE +++ b/LICENSE @@ -1,674 +1,2 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software 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But first, please read -. +YEAR: 2021 +COPYRIGHT HOLDER: Seurat authors diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 000000000..3d63d994c --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,21 @@ +# MIT License + +Copyright (c) 2021 Seurat authors + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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From cd35c15d30811b84b97b83a1c1f1787091e58a30 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Sat, 11 Dec 2021 00:48:15 -0500 Subject: [PATCH 40/53] add sparse row warpper --- R/utilities.R | 65 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) diff --git a/R/utilities.R b/R/utilities.R index 6ae270517..346d55a94 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -2285,6 +2285,71 @@ RemoveLastField <- function(string, delim = "_") { } } +# Calculate row mean of a sparse matrix +# @param mat sparse matrix +# @return A vector of row mean +# +RowMeanSparse <- function(mat) { + mat <- RowSparseCheck(mat = mat) + output <- row_mean_dgcmatrix( + x = slot(object = mat, name = "x"), + i = slot(object = mat, name = "i"), + rows = nrow(x = mat), + cols = ncol(x = mat) + ) + names(x = output) <- rownames(x = mat) + return(output) +} + +# Calculate row sum of a sparse matrix +# +# @param mat sparse matrix +# @return A vector of row sum +# +RowSumSparse <- function(mat) { + mat <- RowSparseCheck(mat = mat) + output <- row_sum_dgcmatrix( + x = slot(object = mat, name = "x"), + i = slot(object = mat, name = "i"), + rows = nrow(x = mat), + cols = ncol(x = mat) + ) + names(x = output) <- rownames(x = mat) + return(output) +} + +# Calculate row variance of a sparse matrix +# +# @param mat sparse matrix +# @return A vector of row variance +# +RowVarSparse <- function(mat) { + mat <- RowSparseCheck(mat = mat) + output <- row_var_dgcmatrix( + x = slot(object = mat, name = "x"), + i = slot(object = mat, name = "i"), + rows = nrow(x = mat), + cols = ncol(x = mat) + ) + names(x = output) <- rownames(x = mat) + return(output) +} + +# Check if the input matrix is dgCMatrix +# +# @param mat sparse matrix +# @return A dgCMatrix +# +RowSparseCheck <- function(mat) { + if (!inherits(x = mat, what = "sparseMatrix")) { + stop("Input should be sparse matrix") + } else if (class(x = mat) != "dgCMatrix") { + warning("Input matrix is converted to dgCMatrix.") + mat <- as.sparse(x = mat) + } + return(mat) +} + # Sweep out array summaries # # Reimplmentation of \code{\link[base]{sweep}} to maintain compatability with From 64297678a67220ae6f8ea67f419368b56afffeeb Mon Sep 17 00:00:00 2001 From: yuhanH Date: Sat, 11 Dec 2021 00:57:09 -0500 Subject: [PATCH 41/53] remove sparseMatrixStats --- NAMESPACE | 1 - R/dimensional_reduction.R | 4 ++-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index 009f4728c..27184a322 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -650,7 +650,6 @@ importFrom(shiny,sliderInput) importFrom(shiny,stopApp) importFrom(shiny,updateSelectInput) importFrom(shiny,verbatimTextOutput) -importFrom(sparseMatrixStats,rowVars) importFrom(spatstat.core,markvario) importFrom(spatstat.geom,ppp) importFrom(stats,aggregate) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 1a80085d4..dbd320d13 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -2260,7 +2260,7 @@ L2Norm <- function(vec) { # @param features Features to use as input for the dimensional reduction technique. # Default is variable features # @ param verbose Print messages and warnings -#' @importFrom sparseMatrixStats rowVars +# # PrepDR <- function( object, @@ -2286,7 +2286,7 @@ PrepDR <- function( features <- features.keep if (inherits(x = data.use, what = 'dgCMatrix')) { - features.var <- rowVars(x = data.use[features, ]) + features.var <- RowVarSparse(mat = data.use[features, ]) } else { features.var <- RowVar(x = data.use[features, ]) From d6567ea504141d9586a1fd0a9c714d5856d6a6d9 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Sat, 11 Dec 2021 01:03:55 -0500 Subject: [PATCH 42/53] fix some docu --- R/generics.R | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/R/generics.R b/R/generics.R index 09ced91f8..e286ecded 100644 --- a/R/generics.R +++ b/R/generics.R @@ -444,18 +444,15 @@ RunPCA <- function(object, ...) { #' Run Supervised Latent Semantic Indexing #' #' Run a supervised LSI (SLSI) dimensionality reduction supervised by a -#' cell-cell kernel. SLSI is used to capture a linear transformation that -#' maximizes its dependency to the given cell-cell kernel. +#' cell-cell kernel. SLSI is used to capture a linear transformation of peaks +#' that maximizes its dependency to the given cell-cell kernel. #' #' @param object An object #' @param ... Arguments passed to other methods #' -#' @return Returns Seurat object with the SPCA calculation stored in the +#' @return Returns Seurat object with the SLSI calculation stored in the #' reductions slot -#' @references Barshan E, Ghodsi A, Azimifar Z, Jahromi MZ. -#' Supervised principal component analysis: Visualization, classification and -#' regression on subspaces and submanifolds. -#' Pattern Recognition. 2011 Jul 1;44(7):1357-71. \url{https://www.sciencedirect.com/science/article/pii/S0031320310005819?casa_token=AZMFg5OtPnAAAAAA:_Udu7GJ7G2ed1-XSmr-3IGSISUwcHfMpNtCj-qacXH5SBC4nwzVid36GXI3r8XG8dK5WOQui}; +#' #' @export #' #' @rdname RunSLSI From e7b1fa82d06e3338535024b2c0ee6615ec3051d4 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Sat, 11 Dec 2021 13:29:01 -0500 Subject: [PATCH 43/53] change default k to 30 --- R/dimensional_reduction.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 19535d4bf..991318aa7 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -335,7 +335,7 @@ ProjectUMAP.default <- function( query.dims = NULL, reference, reference.dims = NULL, - k.param = 20, + k.param = 30, nn.method = "annoy", n.trees = 50, annoy.metric = "cosine", @@ -389,7 +389,7 @@ ProjectUMAP.DimReduc <- function( query.dims = NULL, reference, reference.dims = NULL, - k.param = 20, + k.param = 30, nn.method = "annoy", n.trees = 50, annoy.metric = "cosine", @@ -439,7 +439,7 @@ ProjectUMAP.Seurat <- function( reference, reference.reduction, reference.dims = NULL, - k.param = 20, + k.param = 30, nn.method = "annoy", n.trees = 50, annoy.metric = "cosine", From 9cb461b97699667651084e324e9036d8969d27a1 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Sat, 11 Dec 2021 14:12:34 -0500 Subject: [PATCH 44/53] fix project umap assay warning --- R/dimensional_reduction.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 991318aa7..35cbbe6a6 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -479,6 +479,7 @@ ProjectUMAP.Seurat <- function( neighbor.name = neighbor.name, reduction.model = reference[[reduction.model]], reduction.key = reduction.key, + assay = DefaultAssay(query), ... ) query[[reduction.name]] <- proj.umap$proj.umap From ea83c2d1520c62c109d337786356ab75beceac0c Mon Sep 17 00:00:00 2001 From: yuhanH Date: Sat, 11 Dec 2021 14:21:02 -0500 Subject: [PATCH 45/53] fix IntegrateEmbeddings.transfer warnings --- R/integration.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/integration.R b/R/integration.R index 62150ed1b..5cf4f38ea 100644 --- a/R/integration.R +++ b/R/integration.R @@ -1749,6 +1749,7 @@ IntegrateEmbeddings.TransferAnchorSet <- function( } slot(object = anchorset, name = "object.list") <- object.list new.reduction.name.safe <- gsub(pattern = "_", replacement = "", x = new.reduction.name) + new.reduction.name.safe <- gsub(pattern = "[.]", replacement = "", x = new.reduction.name) slot(object = anchorset, name = "reference.objects") <- 1 anchors <- as.data.frame(x = anchors) anchors$dataset1 <- 1 @@ -3966,7 +3967,7 @@ MapQueryData <- function( X = query.datasets, FUN = function(dataset1) { if (verbose) { - message("Integrating dataset ", dataset1, " with reference dataset") + message("\nIntegrating dataset ", dataset1, " with reference dataset") } filtered.anchors <- anchors[anchors$dataset1 %in% reference.datasets & anchors$dataset2 == dataset1, ] integrated <- RunIntegration( From 61cca80b37848db48e699715bfff3041cf44ddc2 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Sat, 11 Dec 2021 14:25:46 -0500 Subject: [PATCH 46/53] add warning --- R/dimensional_reduction.R | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index 35cbbe6a6..091cf3d4b 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -1386,7 +1386,12 @@ RunUMAP.default <- function( ) } if (is.list(x = object)) { - uwot::umap_transform( + if (ncol(object$idx) != model$n_neighbors) { + warning("Number of neighbors between query and reference ", + "is not equal to the number of neighbros within reference") + model$n_neighbors <- ncol(object$idx) + } + umap_transform( X = NULL, nn_method = object, model = model, From 0eb44d8a81f3eb62af2c0201c79d35d4f886ab23 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Sat, 11 Dec 2021 14:33:33 -0500 Subject: [PATCH 47/53] set k.nn based on reference nn num --- R/integration.R | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/R/integration.R b/R/integration.R index 5cf4f38ea..4982e90e8 100644 --- a/R/integration.R +++ b/R/integration.R @@ -2041,6 +2041,7 @@ MapQuery <- function( message("Query and reference dimensions are not equal, proceeding with reference dimensions.") query.dims <- reference.dims } + ref_nn.num <- Misc(object = reference[[reduction.model]], slot = "model")$n_neighbors query <- do.call( what = ProjectUMAP, args = c(list( @@ -2050,7 +2051,8 @@ MapQuery <- function( reference = reference, reference.dims = reference.dims, reference.reduction = reference.reduction, - reduction.model = reduction.model + reduction.model = reduction.model, + k.param = ref_nn.num ), projectumap.args ) ) From 678c6d998c256ea7841090d4f3cefa6ef4351c1f Mon Sep 17 00:00:00 2001 From: yuhanH Date: Sat, 11 Dec 2021 14:57:40 -0500 Subject: [PATCH 48/53] replace do.call with invoke --- NAMESPACE | 1 + R/integration.R | 20 +++++++++++--------- man/ProjectUMAP.Rd | 6 +++--- 3 files changed, 15 insertions(+), 12 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index c847f2c78..b936e7a62 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -617,6 +617,7 @@ importFrom(reticulate,py_module_available) importFrom(reticulate,py_set_seed) importFrom(rlang,"!!") importFrom(rlang,as_label) +importFrom(rlang,invoke) importFrom(scales,brewer_pal) importFrom(scales,hue_pal) importFrom(scales,rescale) diff --git a/R/integration.R b/R/integration.R index 4982e90e8..e9c64dc7b 100644 --- a/R/integration.R +++ b/R/integration.R @@ -1911,6 +1911,8 @@ LocalStruct <- function( #' reference UMAP using \code{\link{ProjectUMAP}}} #' } #' +#' @importFrom rlang invoke +#' #' @export #' @concept integration #' @@ -2003,9 +2005,9 @@ MapQuery <- function( slot(object = query, name = "tools")$TransferData <- NULL reuse.weights.matrix <- FALSE if (!is.null(x = refdata)) { - query <- do.call( - what = TransferData, - args = c(list( + query <- invoke( + .fn = TransferData, + .args = c(list( anchorset = anchorset, reference = reference, query = query, @@ -2020,9 +2022,9 @@ MapQuery <- function( } } if (anchor.reduction != "cca"){ - query <- do.call( - what = IntegrateEmbeddings, - args = c(list( + query <- invoke( + .fn = IntegrateEmbeddings, + .args = c(list( anchorset = anchorset, reference = reference, query = query, @@ -2042,9 +2044,9 @@ MapQuery <- function( query.dims <- reference.dims } ref_nn.num <- Misc(object = reference[[reduction.model]], slot = "model")$n_neighbors - query <- do.call( - what = ProjectUMAP, - args = c(list( + query <- invoke( + .fn = ProjectUMAP, + .args = c(list( query = query, query.reduction = new.reduction.name, query.dims = query.dims, diff --git a/man/ProjectUMAP.Rd b/man/ProjectUMAP.Rd index 080f1da4f..0e40dc4e4 100644 --- a/man/ProjectUMAP.Rd +++ b/man/ProjectUMAP.Rd @@ -14,7 +14,7 @@ ProjectUMAP(query, ...) query.dims = NULL, reference, reference.dims = NULL, - k.param = 20, + k.param = 30, nn.method = "annoy", n.trees = 50, annoy.metric = "cosine", @@ -31,7 +31,7 @@ ProjectUMAP(query, ...) query.dims = NULL, reference, reference.dims = NULL, - k.param = 20, + k.param = 30, nn.method = "annoy", n.trees = 50, annoy.metric = "cosine", @@ -50,7 +50,7 @@ ProjectUMAP(query, ...) reference, reference.reduction, reference.dims = NULL, - k.param = 20, + k.param = 30, nn.method = "annoy", n.trees = 50, annoy.metric = "cosine", From 6a920f560fc4d06952f95690e211237e7b60eaa1 Mon Sep 17 00:00:00 2001 From: yuhanH Date: Sun, 12 Dec 2021 20:22:24 -0500 Subject: [PATCH 49/53] add ... in default --- R/dimensional_reduction.R | 2 +- R/generics.R | 2 +- man/RunSLSI.Rd | 14 ++++---------- 3 files changed, 6 insertions(+), 12 deletions(-) diff --git a/R/dimensional_reduction.R b/R/dimensional_reduction.R index dbd320d13..8c1352635 100644 --- a/R/dimensional_reduction.R +++ b/R/dimensional_reduction.R @@ -2469,7 +2469,7 @@ RunSLSI.default <- function( if (verbose) { message("Performing eigendecomposition") } - svd.V <- irlba(A = object.smooth, nv = n, nu = n) + svd.V <- irlba(A = object.smooth, nv = n, nu = n, ...) sigma <- sqrt(x = svd.V$d) feature.loadings <- object %*% (graph %*% svd.V$u) %*% diag(x = 1/sigma) feature.loadings <- as.matrix(x = feature.loadings) diff --git a/R/generics.R b/R/generics.R index e286ecded..f1a10e795 100644 --- a/R/generics.R +++ b/R/generics.R @@ -448,7 +448,7 @@ RunPCA <- function(object, ...) { #' that maximizes its dependency to the given cell-cell kernel. #' #' @param object An object -#' @param ... Arguments passed to other methods +#' @param ... Arguments passed to IRLBA irlba #' #' @return Returns Seurat object with the SLSI calculation stored in the #' reductions slot diff --git a/man/RunSLSI.Rd b/man/RunSLSI.Rd index 05f716857..c89ed6886 100644 --- a/man/RunSLSI.Rd +++ b/man/RunSLSI.Rd @@ -48,7 +48,7 @@ RunSLSI(object, ...) \arguments{ \item{object}{An object} -\item{...}{Arguments passed to other methods} +\item{...}{Arguments passed to IRLBA irlba} \item{assay}{Name of Assay SLSI is being run on} @@ -69,18 +69,12 @@ using the variable features for the Assay.} \item{reduction.name}{dimensional reduction name} } \value{ -Returns Seurat object with the SPCA calculation stored in the +Returns Seurat object with the SLSI calculation stored in the reductions slot } \description{ Run a supervised LSI (SLSI) dimensionality reduction supervised by a -cell-cell kernel. SLSI is used to capture a linear transformation that -maximizes its dependency to the given cell-cell kernel. -} -\references{ -Barshan E, Ghodsi A, Azimifar Z, Jahromi MZ. -Supervised principal component analysis: Visualization, classification and -regression on subspaces and submanifolds. -Pattern Recognition. 2011 Jul 1;44(7):1357-71. \url{https://www.sciencedirect.com/science/article/pii/S0031320310005819?casa_token=AZMFg5OtPnAAAAAA:_Udu7GJ7G2ed1-XSmr-3IGSISUwcHfMpNtCj-qacXH5SBC4nwzVid36GXI3r8XG8dK5WOQui}; +cell-cell kernel. SLSI is used to capture a linear transformation of peaks +that maximizes its dependency to the given cell-cell kernel. } \concept{dimensional_reduction} From 393ec7daffcfa12455588d4c0dd4b70f7895c33a Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Tue, 14 Dec 2021 14:27:06 -0500 Subject: [PATCH 50/53] Update changelog Bump develop version --- DESCRIPTION | 4 ++-- NEWS.md | 2 ++ 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index cdd6bc431..a9b8ad0e1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Seurat -Version: 4.0.5.9004 -Date: 2021-12-03 +Version: 4.0.5.9005 +Date: 2021-12-14 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 7a4a59d16..6f016a5b5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,8 @@ # Unreleased ## Added +- Implement supervised LSI + ## Changes - Add `raster` parameter to `VlnPlot` to optionally rasterize individual points ([#5076](https://github.com/satijalab/seurat/pull/5076)) - Add `min.cells.group` parameter to `FindConservedMarkers` ([#5079](https://github.com/satijalab/seurat/pull/5079)) From b42f1a13d73ab7c96e1a4c95791f02eb07f5e16e Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Tue, 14 Dec 2021 15:24:41 -0500 Subject: [PATCH 51/53] Update changelog Bump develop version --- DESCRIPTION | 2 +- NEWS.md | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index a9b8ad0e1..b7fb60b5f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: Seurat -Version: 4.0.5.9005 +Version: 4.0.5.9006 Date: 2021-12-14 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. diff --git a/NEWS.md b/NEWS.md index 6f016a5b5..fa8f7e1b2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -9,6 +9,7 @@ - Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors` - Fix error message in `ReadMtx()` ([#5158](https://github.com/satijalab/seurat/issues/5158)) - Add `label.color` parameter to `FeaturePlot` ([#5314](https://github.com/satijalab/seurat/pull/5314)) +- Fix issues in `ProjectUMAP` ([#5257](https://github.com/satijalab/seurat/issues/5257), [#5104](https://github.com/satijalab/seurat/issues/5104), [#5373](https://github.com/satijalab/seurat/issues/5373)) # Seurat 4.0.5 (2020-10-04) ## Changes From 85fbc292ca7554ab9c332021be559214cf78641f Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Thu, 16 Dec 2021 10:58:37 -0500 Subject: [PATCH 52/53] Bump version --- DESCRIPTION | 4 ++-- NEWS.md | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b7fb60b5f..ca4569e1f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: Seurat -Version: 4.0.5.9006 -Date: 2021-12-14 +Version: 4.0.6 +Date: 2021-12-16 Title: Tools for Single Cell Genomics Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) , Macosko E, Basu A, Satija R, et al (2015) , Stuart T, Butler A, et al (2019) , and Hao, Hao, et al (2020) for more details. Authors@R: c( diff --git a/NEWS.md b/NEWS.md index fa8f7e1b2..2877cc185 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# Unreleased +# Seurat 4.0.6 (2021-12-16) ## Added - Implement supervised LSI @@ -11,14 +11,14 @@ - Add `label.color` parameter to `FeaturePlot` ([#5314](https://github.com/satijalab/seurat/pull/5314)) - Fix issues in `ProjectUMAP` ([#5257](https://github.com/satijalab/seurat/issues/5257), [#5104](https://github.com/satijalab/seurat/issues/5104), [#5373](https://github.com/satijalab/seurat/issues/5373)) -# Seurat 4.0.5 (2020-10-04) +# Seurat 4.0.5 (2021-10-04) ## Changes - Update documentation for `to.upper` parameter in `Load10X_Spatial()` ([#4576](https://github.com/satijalab/seurat/issues/4576)) - Update concept tags for `RunSPCA()` ([#4978](https://github.com/satijalab/seurat/discussions/4987)) - Conditionally run tests/packages that use suggested packages ([#5160](https://github.com/satijalab/seurat/pull/5160)) - Set random state in `RunUMAP()` when using the `umap-learn` method ([#5194](https://github.com/satijalab/seurat/issues/5194)) -# Seurat 4.0.4 (2020-08-19) +# Seurat 4.0.4 (2021-08-19) ## Added - Add `reduction` parameter to `BuildClusterTree()` ([#4598](https://github.com/satijalab/seurat/issues/4598)) - Add DensMAP option to `RunUMAP()` ([#4630](https://github.com/satijalab/seurat/pull/4630)) From 288f5c0467a464bbb5428e726b231158bcd658a1 Mon Sep 17 00:00:00 2001 From: Paul Hoffman Date: Thu, 16 Dec 2021 11:18:24 -0500 Subject: [PATCH 53/53] Update CRAN comments --- cran-comments.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 8ae6a6d5b..5799d0411 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,7 +1,7 @@ -# Seurat v4.0.5 +# Seurat v4.0.6 ## Test environments -* local Ubuntu 20.04 install, R 4.1.0 +* local Ubuntu 20.04 install, R 4.1.2 * Ubuntu 16.04.6 (on travis-ci), R 4.0.0, R devel * macOS 10.13.6 (on travis-ci), R 4.0.2 * Windows Server 2012 R2 (on AppVeyor), R 4.1.0 Patched @@ -12,8 +12,8 @@ There were no ERRORs, WARNINGs, or NOTEs ## Downstream dependencies -There is one package that depends on Seurat: tidyseurat; this update does not impact its functionality +There no packages that depend on Seurat -There are ten packages that import Seurat: CDSeq, DUBStepR, PhitestR, rPanglaoDB, scDiffCom, scMappR, scRNAstat, Signac, SignacX, and SoupX; this update does not impact their functionality +There are sixteen packages that import Seurat: CAMML, CDSeq, CIDER, DR.SC, DUBStepR, PhitestR, Platypus, rPanglaoDB, scDiffCom, scMappR, SCRIP, scRNAstat, Signac, SignacX, SoupX, and tidyseurat; this update does not impact their functionality There are ten packages that suggest Seurat: BisqueRNA, ClustAssess, clustree, conos, DIscBIO, dyngen, harmony, rliger, Rmagic, and VAM; this update does not impact their functionality.