address #75, #99, bump cell2cell, fix edgecase

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: liana
 Type: Package
 Title: LIANA: a LIgand-receptor ANalysis frAmework
-Version: 0.1.12
+Version: 0.1.13
 Authors@R: c(
     person(
         given = "Daniel",
@@ -91,5 +91,5 @@ Suggests:
     broom
 biocViews: scater, scran, SingleCellExperiment, ComplexHeatmap, muscData, ExperimentHub
 Remotes: sqjin/CellChat, saezlab/OmnipathR, saezlab/decoupleR, LTLA/basilisk.utils, LTLA/basilisk
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3

NEWS.md

@@ -1,4 +1,16 @@
-# LIANA 0.1.12 (24.02.22)
+# LIANA 0.1.13 (03.11.23)
+
+- Changed the way that `max` rank is imputed when NAs are presented, or when `return_all` is true. 
+Essentially, `RobustRankAggregate` will use the max rank in the matrix, rather than the size of the dataframe.
+
+- Fixed a bug related to newer versions of CellChat with unused argument #75
+
+- Bumped `cell2cell` to its latest `0.6.8` version.
+
+- LIANA's `source` and `target` will not inherit the levels of `idents_col` #99
+
+
+# LIANA 0.1.12 (24.02.23)
 
 - Added `rank_aggregate` to generate both specificity and magnitude rank
 aggregates. Essentially runs `liana_aggregate` twice with different `aggregate_how`
@@ -14,7 +26,7 @@ scores to Tensor format.
 - Added additional tests related to Tensor-cell2cell
 
 
-# LIANA 0.1.11 (06.02.22)
+# LIANA 0.1.11 (06.02.23)
 
 - Fixed issue with sample_col in `liana_tensor` functions
 - Removed redundant scconnect code
@@ -23,7 +35,7 @@ scores to Tensor format.
 - passing "all" to `select_resource` will now only return human resources.
 - add minor condition improvements to `liana_wrap` PR#92
 
-# LIANA 0.1.10 (23.01.22)
+# LIANA 0.1.10 (23.01.23)
 
 - Fixed issues in the `generate_lr_geneset` function, and other typos and
 by mistake hardcoded values.

R/cellchat_pipe.R

@@ -120,7 +120,6 @@ call_cellchat <- function(sce,
     cellchat.omni <- CellChat::computeCommunProb(cellchat.omni,
                                                  raw.use = .raw_use,
                                                  seed.use = .seed,
-                                                 do.fast = TRUE,
                                                  nboot = nboot)
 
     # Filter out the cell-cell communication if there are only few number of cells in certain cell groups

R/liana_aggregate.R

@@ -276,71 +276,32 @@ rank_aggregate <- function(liana_res, ...){
 .aggregate_rank <- function(liana_mlist, join_cols, verbose, ...){
     liana_message("Aggregating Ranks", output = "message", verbose = verbose)
 
-    liana_mlist %>%
+    rankmat <- liana_mlist %>%
         map(function(res){
-            # bad practice, but almost unavoidable here...
             res %>%
                 unite(join_cols,
                       col = "interaction",
                       sep = "⊎") %>%
-                pull("interaction")
+                select(interaction, ends_with("rank"))
         }) %>%
-        .rank_matrix %>%
+        reduce(full_join,  by="interaction")  %>%
+        column_to_rownames(var = "interaction") %>%
+        as.matrix()
+
+    rankmat[is.na(rankmat)] <- max(rankmat, na.rm=TRUE)
+
+    rankmat %>%
+        {. / max(.)} %>%
         .robust_rank_agg(.,
                          ...) %>%
         separate(col = "interaction", sep = "⊎",
                  into = join_cols)
 }
 
 
-
-#' Function to convert a list of characters to a ranked matrix [0,1]
-#'
-#' @param glist a list of ranked/ordered characters
-#'
-#' @return a matrix filled with 0-1 values depending on the position order
-#' of the characters.
-#'
-#' @details Adated from Kolde et al., 2012.
-#' Required due to the removal of the RobustRankAggregate package from CRAN.
-#'
-#' @references Kolde, R., Laur, S., Adler, P. and Vilo, J., 2012.
-#'  Robust rank aggregation for gene list integration and meta-analysis.
-#'  Bioinformatics, 28(4), pp.573-580.
-#'
-#' @keywords internal
-.rank_matrix <- function(glist, ...){
-
-    # Get unique entities
-    u.ents <- unique(c(glist, recursive = TRUE))
-
-    # num of entities per col
-    num.ents <- length(u.ents)
-
-    # get position for each vect
-    pos.mat <- sapply(FUN = match,
-                      X = glist,
-                      x = u.ents,
-                      nomatch = num.ents) %>%
-        matrix(nrow = num.ents,
-               ncol = length(glist),
-               dimnames = list(u.ents, names(glist)))
-
-    # Fill mat /w total ents
-    rank.mat <- matrix(num.ents,
-                       nrow = num.ents,
-                       ncol = length(glist),
-                       dimnames = list(u.ents, names(glist)))
-
-    # return rank/total_rank by pos
-    return(pos.mat / rank.mat)
-
-}
-
-
 #' Function to calculate and format aggregate ranks
 #'
-#' @param rmat ranked matrix formated with `.rank_matrix`
+#' @param rmat a ranked matrix [0,1]
 #'
 #' @details Adated from Kolde et al., 2012.
 #' Required due to the removal of the RobustRankAggregate package from CRAN.

R/liana_pipe.R

@@ -196,7 +196,6 @@ liana_pipe <- function(sce,
             .sp_costrain(cell.adj)
     }
 
-
     # Join complexes (recomplexify) to lr_res
     cmplx <- op_resource %>%
         select(
@@ -211,6 +210,10 @@ liana_pipe <- function(sce,
                   by=c("ligand", "receptor")) %>%
         distinct()
 
+    # Inherit levels of idents
+    levels(lr_res$source) <- levels(colLabels(sce))
+    levels(lr_res$target) <- levels(colLabels(sce))
+
     return(lr_res)
 }
 

R/liana_tensor.R

@@ -902,5 +902,5 @@ decompose_tensor <- function(tensor,
                        "pandas==1.4.2",
                        "rpy2==3.4.5")
 
-.liana_pips <- c("cell2cell==0.6.3",
+.liana_pips <- c("cell2cell==0.6.8",
                  "anndata2ri==1.0.6")

tests/testthat/test-liana_aggr.R

@@ -10,7 +10,7 @@ test_that("Test liana aggregate", {
                               "output", "liana_res.RDS")) %>%
         liana_aggregate()
 
-    expect_equal(exp1, res1)
+    expect_equal(res1, exp1)
 })
 
 
@@ -27,7 +27,7 @@ test_that("Test liana aggregate (housekeep)", {
     )
 
 
-    expect_equal(exp2, res2)
+    expect_equal(res2, exp2)
 })
 
 

tests/testthat/test-liana_cpdb.R

@@ -14,3 +14,4 @@ test_that("Test liana cpdb", {
 
     expect_equal(exp1, res1)
 })
+

tests/testthat/test-liana_cytotalk.R

@@ -12,5 +12,5 @@ test_that("Test Cytotalk Wrap", {
                        method = c('cytotalk'),
                        resource = c('OmniPath'))
 
-    expect_equal(exp1, res1)
+    expect_equal(res1, exp1)
 })