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functions_helpers.R
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functions_helpers.R
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color2 <- function()
{
color2 <- c("#8DD3C7", "#FFFFB3", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F",
"#7FC97F", "#BEAED4", "#FDC086", "#E6AB02", "#386CB0", "#A6761D", "#F0027F", "#BF5B17", "#666666", "#1B9E77", "#D95F02",
"#7570B3", "#E7298A", "#66A61E", "#FFFF99", "#BEBADA")
color2
}
Heatmap_log10FDRvsAge <- function(variable, AgeWaves)
{
tmp <- AgeWaves[[variable]]
tmp[is.na(tmp)] <- 0#3
tmp[tmp < 0] <- 0
tmp[sapply(tmp, is.infinite)] <- NA
maxtmp <- max(tmp, na.rm = T)
tmp[is.na(tmp)] <- maxtmp + 2 # to ease visualization, use Inf values as the maximum value + 2 (significant for sure)
#tmp <- as.matrix(tmp[order(row.names(tmp)), ])
#tmp[tmp < 0] <- 0
i <- (hclust(dist(tmp)))
#browser()
tmp <- as.matrix(tmp[i$order, ])
tmp <- melt(tmp)
colnames(tmp) <- c("tissue", "age", "-log10(FDR)")
ClickFunction <- JS("function(event) {Shiny.onInputChange('tissueClicked', event.point.tissue) }")
ClickFunction2 <- JS("function(event) {console.log(event) }")
g <- hchart(tmp, type = "heatmap", boost = list(useGPUTranslations = T),
hcaes(x = age, y = tissue, value = `-log10(FDR)`)) %>%
hc_colorAxis(stops = color_stops(100, rev(magma(100))),
min = 0,
reversed = F) %>%
hc_legend(layout = "vertical", verticalAlign = "top",
align = "right", title = list(text = "-log<sub>10</sub>(FDR) <br/> <i><small> Proportion altered genes <i/><small/>", style = list(fontSize = '16px')), useHTML = TRUE) %>%
hc_xAxis(title = list(text = "Age (years)", style = list(fontSize = '18px')),
labels = list(style = list(fontSize = "14px"))) %>%
hc_yAxis(title = list(text = "Tissue", style = list(fontSize = '18px')), reversed = TRUE) %>%
hc_tooltip(formatter = JS("function(){return '<b>Age</b>: ' + this.point.x + ' y.o., <br><b>Tissue</b>: ' + this.series.yAxis.categories[this.point.y] + ',<br><b> -log<sub>10</sub>(FDR)</b>: ' + Highcharts.numberFormat(this.point.value, 2);}"), useHTML = T) %>%
hc_plotOptions(series = list(events = list(click = ClickFunction)))
return(g)
}
Line_sigGenesvsAge <- function(tissue, variable, peak)
{
tmp <- peak[peak$tissue == tissue & peak$variable == variable,]
tmp$pvalue[tmp$pvalue == 0] <- 1e-6
tmp$log10p <- -log10(tmp$pvalue)
ClickFunction <- JS("function(event) {Shiny.onInputChange('peakClicked', event.point.age)
Shiny.onInputChange('peakClickedState', event.point.state)
Shiny.onInputChange('peakClickedVariable', event.point.series.name)}")
ClickFunction2 <- JS("function(event) {console.log(event) }")
if (max(tmp$log10p)< -log10(0.05)){
max_scale <- -log10(0.05)
} else {
max_scale <- max(tmp$log10p)
}
tmp$mycolor <- circlize::colorRamp2(breaks = c(0, max_scale/2, max_scale), colors = c("#dfe59a", "#9dca94", "#346875"))(tmp$log10p)
g <- hchart(tmp, "scatter", hcaes(x = age, y = PercSigGene,
color = mycolor), name = variable) %>%
hc_plotOptions(series = list(allowPointSelect = TRUE,
lineWidth = 6,
color = "black",
marker = list(radius = 8, enabled = T,
states = list(select = list(fillColor = "tomato", lineWidth = 0, radius = 14))),
events = list(click = ClickFunction))) %>%
hc_colorAxis(stops = list(list(0, "#dfe59a"), list(0.5, "#9dca94"), list(1, "#346875")),
min = 0, max = max(tmp$log10p)) %>%
hc_legend(layout = "horizontal", reversed = T,
align = "center", title = list(text = "-log<sub>10</sub>(FDR)"), useHTML = TRUE) %>%
hc_xAxis(title = list(text = "Age (years)"), min = 20, max = 70) %>%
hc_yAxis(title = list(text = "% altered genes")) %>%
hc_tooltip(formatter = JS("function(){return '<b>Age</b>: ' + this.point.age + ' y.o., <br><b>%alt genes</b>: ' + Highcharts.numberFormat(this.point.PercSigGene, 2) + ',<br><b> -log<sub>10</sub>(FDR)</b>: ' + Highcharts.numberFormat(this.point.options.log10p, 2);}"), useHTML = TRUE)
return(g)
}
Line_pvaluevsAge <- function(gene, pvalueData, geneData, allAges, abline, tissue, coloredBy)
{
#GE info
GE <- geneData
GE <- GE[GE$tissue == tissue,]
GE$jittered_age <- jitter_ages(GE$age)
#statsAllAges_text <- paste0("Overall changes: p-value = ", round(allAges$pvalue,4), " | t-statistic = ", round(allAges$tvalue,2))
statsAllAges_text <- paste0("Overall changes: p-value = ", round(allAges$pvalue,4), " | t-statistic = ", round(allAges$tvalue,2), " | logFC/year = ", round(abline$a,4))
if (coloredBy == "Age")
{
fit_abline <- data.frame(x=seq(20,70,0.1),
y=abline$a * (seq(20,70,0.1) - mean(GE$age))+ abline$b)
fit <- loess(expression ~ age, data = GE)
fit <- plyr::arrange(generics::augment(fit), age)
#Pvalue info
tmp <- melt(as.matrix(pvalueData[rownames(pvalueData) == gene,]))
colnames(tmp) <- c("gene", "Age", "p-value")
tmp$log10p <- -log10(tmp$`p-value`)
g <- highchart() %>%
hc_yAxis_multiples(
list(lineWidth = 2, title = list(useHTML = TRUE, text = "log<sub>10</sub>(p-value)", style = list(color = "#9A839A")), lineColor = "#9A839A", labels = list(style = list(color = "#9A839A")), height = "50%",
plotLines = list(list(value = 1.3, color = "black", width = 3, dashStyle = "dot", label = list(text = "p = 0.05")),
list(value = 2, color = "black", width = 3, dashStyle = "dot", label = list(text = "p = 0.01")))),
list(showLastLabel = FALSE, opposite = TRUE, title = list(text = "GE (logCPM)", style = list(color = "yellowgreen")), height = "50%", top = "50%",
lineColor = "yellowgreen", lineWidth = 2,
labels = list(style = list(color = "yellowgreen")))
) %>%
hc_add_series(data = list_parse2(GE[, c("jittered_age", "expression")]), type = "scatter", showInLegend = FALSE,
yAxis = 1, color = "yellowgreen", marker = list(radius = 4, symbol = "round")) %>%
# hc_add_series(data = list_parse2(data.frame(fit$age, fit$.fitted - 2*fit$.se.fit, fit$.fitted + 2*fit$.se.fit)), yAxis = 1,
# type = "arearange", showInLegend = FALSE, color = "lightgrey") %>%
hc_add_series(data = list_parse2(data.frame(fit$age, fit$.fitted)), yAxis = 1, lineWidth = 5,
type = "line", showInLegend = FALSE, color = "black") %>%
hc_add_series(data = list_parse2(tmp[, c("Age", "log10p")]), type = "line", showInLegend = FALSE, name = "log10p",
color = "#9A839A", marker = list(radius = 6, enabled = T, color = "black"), lineWidth = 5) %>%
hc_xAxis(title = list(text = "Age (years)"), lineColor = "grey", min = 20, max = 70) %>%
hc_tooltip(formatter = JS("function(){
if(this.point.series.name == 'log10p'){
return '<b>Age</b>: ' + this.point.x + ' y.o., <br><b>log<sub>10</sub>(p-value)</b>: ' + Highcharts.numberFormat(this.point.y, 2);}
else{return '<b>Age</b>: ' + this.point.x + ' y.o., <br><b>GE</b>: ' + Highcharts.numberFormat(this.point.y, 2) + ' logCPM';}
}"), useHTML = TRUE)%>%
hc_add_series(
data = list_parse2(data.frame(fit_abline$x, fit_abline$y)),
type = "line",
showInLegend = FALSE,
yAxis = 1,
name = "Entire Age Range",
color = "#E9724C", # Set the line color to blue
lineWidth = 10, # Set the line width
dashStyle = "dot", # Set the line style to dotted
marker = list(radius = 0, symbol = "round")
) %>%
hc_subtitle(text = statsAllAges_text, style = list(color = "#E9724C") )
} else if (coloredBy == "Gender") {
statsAllAges_text <- paste0("Overall changes: p-value = ", round(allAges$pvalue,4), " | t-statistic = ", round(allAges$tvalue,2), " | logFC = ", round(abline$a,4)) #Change the logFC/year to logFC
fit_male <- loess(expression ~ age, data = GE[GE$sex == 1,])
fit_male <- plyr::arrange(generics::augment(fit_male), age)
fit_female <- loess(expression ~ age, data = GE[GE$sex == 2,])
fit_female <- plyr::arrange(generics::augment(fit_female), age)
#Pvalue info
tmp <- melt(as.matrix(pvalueData[rownames(pvalueData) == gene,]))
colnames(tmp) <- c("gene", "Age", "p-value")
tmp$log10p <- -log10(tmp$`p-value`)
x <- mean(GE$age)
stats_male <- data.frame(x=x,
y=abline$a * (1 - mean(GE$sex)) + abline$b)
stats_female <- data.frame(x=x,
y=abline$a * (2 - mean(GE$sex)) + abline$b)
g <- highchart() %>%
hc_yAxis_multiples(
list(lineWidth = 2, title = list(useHTML = TRUE, text = "log<sub>10</sub>(p-value)", style = list(color = "#9A839A")), lineColor = "#9A839A", labels = list(style = list(color = "#9A839A")), height = "50%",
plotLines = list(list(value = 1.3, color = "black", width = 1, dashStyle = "dot", label = list(text = "p = 0.05")),
list(value = 2, color = "black", width = 1, dashStyle = "dot", label = list(text = "p = 0.01")))),
list(showLastLabel = FALSE, opposite = TRUE, height = "50%", top = "50%",
title = list(text = "GE (logCPM)", style = list(color = "grey")),
lineColor = "grey", lineWidth = 2,
labels = list(style = list(color = "grey")))
) %>%
hc_add_series(data = list_parse2(GE[GE$sex == 1, c("jittered_age", "expression")]), type = "scatter", name = "Male",
yAxis = 1, color = "cornflowerblue", marker = list(radius = 4, symbol = "round")) %>%
hc_add_series(data = list_parse2(GE[GE$sex == 2, c("jittered_age", "expression")]), type = "scatter", name = "Female",
yAxis = 1, color = "hotpink", marker = list(radius = 4, symbol = "round")) %>%
hc_add_series(data = list_parse2(data.frame(fit_male$age, fit_male$.fitted)), yAxis = 1, lineWidth = 5,
type = "line", showInLegend = FALSE, color = "cornflowerblue") %>%
hc_add_series(data = list_parse2(data.frame(fit_female$age, fit_female$.fitted)), yAxis = 1, lineWidth = 5,
type = "line", showInLegend = FALSE, color = "hotpink") %>%
hc_add_series(data = list_parse2(tmp[, c("Age", "log10p")]), type = "line", showInLegend = FALSE, name = "log10p",
color = "#9A839A", marker = list(radius = 6, enabled = T, color = "black"), lineWidth = 5) %>%
hc_xAxis(title = list(text = "Age (years)"), lineColor = "grey", min = 20, max = 70) %>%
hc_tooltip(formatter = JS("function(){
if(this.point.series.name == 'log10p'){
return '<b>Age</b>: ' + this.point.x + ' y.o., <br><b>log<sub>10</sub>(p-value)</b>: ' + Highcharts.numberFormat(this.point.y, 2);}
else{return '<b>Age</b>: ' + this.point.x + ' y.o., <br><b>GE</b>: ' + Highcharts.numberFormat(this.point.y, 2) + ' logCPM';}
}"), useHTML = TRUE)%>%
hc_add_series(
data = list_parse2(data.frame(stats_male$x, stats_male$y)),
type = "scatter",
showInLegend = FALSE,
yAxis = 1,
name = "Entire Age Range (male)",
color = "blue",
marker = list(radius = 10, symbol = "cross")
)%>%
hc_add_series(
data = list_parse2(data.frame(stats_female$x, stats_female$y)),
type = "scatter",
showInLegend = FALSE,
yAxis = 1,
name = "Entire Age Range (female)",
color = "mediumvioletred", # Set the line color to blue
marker = list(radius = 10, symbol = "cross")
) %>%
hc_subtitle(text = statsAllAges_text, style = list(color = "black") )
} else {
statsAllAges_text <- paste0("Overall changes: p-value = ", round(allAges$pvalue,4), " | t-statistic = ", round(allAges$tvalue,2), " | logFC/year = ", round(abline$a,4)) #Change the logFC/year to logFC
fit_male <- loess(expression ~ age, data = GE[GE$sex == 1,])
fit_male <- plyr::arrange(generics::augment(fit_male), age)
fit_female <- loess(expression ~ age, data = GE[GE$sex == 2,])
fit_female <- plyr::arrange(generics::augment(fit_female), age)
#Pvalue info
tmp <- melt(as.matrix(pvalueData[rownames(pvalueData) == gene,]))
colnames(tmp) <- c("gene", "Age", "p-value")
tmp$log10p <- -log10(tmp$`p-value`)
g <- highchart() %>%
hc_yAxis_multiples(
list(lineWidth = 2, title = list(useHTML = TRUE, text = "log<sub>10</sub>(p-value)", style = list(color = "#9A839A")), lineColor = "#9A839A", labels = list(style = list(color = "#9A839A")), height = "50%",
plotLines = list(list(value = 1.3, color = "black", width = 1, dashStyle = "dot", label = list(text = "p = 0.05")),
list(value = 2, color = "black", width = 1, dashStyle = "dot", label = list(text = "p = 0.01")))),
list(showLastLabel = FALSE, opposite = TRUE, height = "50%", top = "50%",
title = list(text = "GE (logCPM)", style = list(color = "grey")),
lineColor = "grey", lineWidth = 2,
labels = list(style = list(color = "grey")))
) %>%
hc_add_series(data = list_parse2(GE[GE$sex == 1, c("jittered_age", "expression")]), type = "scatter", name = "Male",
yAxis = 1, color = "cornflowerblue", marker = list(radius = 4, symbol = "round")) %>%
hc_add_series(data = list_parse2(GE[GE$sex == 2, c("jittered_age", "expression")]), type = "scatter", name = "Female",
yAxis = 1, color = "hotpink", marker = list(radius = 4, symbol = "round")) %>%
hc_add_series(data = list_parse2(data.frame(fit_male$age, fit_male$.fitted)), yAxis = 1, lineWidth = 5,
type = "line", showInLegend = FALSE, color = "cornflowerblue") %>%
hc_add_series(data = list_parse2(data.frame(fit_female$age, fit_female$.fitted)), yAxis = 1, lineWidth = 5,
type = "line", showInLegend = FALSE, color = "hotpink") %>%
hc_add_series(data = list_parse2(tmp[, c("Age", "log10p")]), type = "line", showInLegend = FALSE, name = "log10p",
color = "#9A839A", marker = list(radius = 6, enabled = T, color = "black"), lineWidth = 5) %>%
hc_xAxis(title = list(text = "Age (years)"), lineColor = "grey", min = 20, max = 70) %>%
hc_tooltip(formatter = JS("function(){
if(this.point.series.name == 'log10p'){
return '<b>Age</b>: ' + this.point.x + ' y.o., <br><b>log<sub>10</sub>(p-value)</b>: ' + Highcharts.numberFormat(this.point.y, 2);}
else{return '<b>Age</b>: ' + this.point.x + ' y.o., <br><b>GE</b>: ' + Highcharts.numberFormat(this.point.y, 2) + ' logCPM';}
}"), useHTML = TRUE) %>%
hc_subtitle(text = statsAllAges_text, style = list(color = "black") )
}
# g <- g%>%
# hc_subtitle(text = statsAllAges_text, style = list(color = "black") )
return(g)
}
jitter_ages <- function(agevec){
set.seed(123456)
# Create age bins, compatible to those used in the public metadata
bins <- cut(agevec, breaks = seq(20, 70, 5), include.lowest = TRUE)
# Compute bin midpoints (mean of each bin)
bin_midpoints <- as.numeric(tapply(agevec, bins, function(x) mean(range(x))))
# Replace values with bin midpoints
new_values <- bin_midpoints[(bins)]
# Add jitter within 5-year window
jittered_values <- jitter(new_values, amount = 2.5) # half the bin width
# Ensure values stay within 20 and 70
jittered_values[jittered_values < 20] <- 20
jittered_values[jittered_values > 70] <- 70
return(jittered_values)
}
scatter_GEvsAge <- function(data, tissue, colored, shaped, donorCondition, gene, geneInfo)
{
#tmp <- dbGetQuery(DBconnection, paste("SELECT * FROM", gene, sep = " "))
tmp <- data
tmp <- tmp[tmp$tissue == tissue,]
tmp$jittered_age <- jitter_ages(tmp$age)
#To zoom the plot onto a selected area
#Removed so age can't be found to respect GTEx rules
#To remove the possibility to subset some donor GE, comment , zoomType = 'xy' , events = list(selection = SelectFunction) in the functions
SelectFunction <- JS("function(event) {
var x_axis_min,x_axis_max,y_axis_min,y_axis_max;
if (event.xAxis) {
x_axis_min = Highcharts.numberFormat(event.xAxis[0].min, 2),
x_axis_max = Highcharts.numberFormat(event.xAxis[0].max, 2);
}else{
x_axis_min = 'reset',
x_axis_max = 'reset';
}
if (event.yAxis) {
y_axis_min = Highcharts.numberFormat(event.yAxis[0].min, 2),
y_axis_max = Highcharts.numberFormat(event.yAxis[0].max, 2);
}else{
y_axis_min = 'reset',
y_axis_max = 'reset';
}
Shiny.onInputChange('Selectedxmin', x_axis_min);
Shiny.onInputChange('Selectedxmax', x_axis_max);
Shiny.onInputChange('Selectedymin', y_axis_min);
Shiny.onInputChange('Selectedymax', y_axis_max);
}")
ClickFunction <- JS("function(event) {Shiny.onInputChange('ClickedIndex', event.point.index)
Shiny.onInputChange('ClickedStatus', event.point.state)}")
ClickFunction2 <- JS("function(event) {console.log(event) }")
if (colored == "none" & shaped == "none")
{
fit <- loess(expression ~ age, data = tmp)
fit <- plyr::arrange(generics::augment(fit), age)
g <- highchart() %>%
hc_chart(type = 'scatter'
, zoomType = 'xy'
, events = list(selection = SelectFunction)
) %>%
hc_add_series(data = list_parse2(tmp[, c("jittered_age", "expression")]), showInLegend = FALSE) %>%
# hc_add_series(data = list_parse2(data.frame(fit$age, fit$.fitted - 2*fit$.se.fit, fit$.fitted + 2*fit$.se.fit)),
# type = "arearange", showInLegend = FALSE) %>%
hc_add_series(data = list_parse2(data.frame(fit$age, fit$.fitted)),
type = "line", showInLegend = FALSE) %>%
hc_plotOptions(arearange = list(color = "gainsboro", opacity = 0.005),
line = list(lineWidth = 7, color = "black"),
scatter = list(marker = list(radius = 5, symbol = "line"), color = "yellowgreen"),
series = list(allowPointSelect = TRUE,
events = list(click = ClickFunction),
marker = list(states = list(select = list(fillColor = "lightgrey", lineWidth = 1, radius = 6, lineColor = "black")))))
} else if (colored == "Sex" & shaped == "none")
{
if (nrow(tmp[tmp$sex == 1,])!=0)
{
fit_male <- loess(expression ~ age, data = tmp[tmp$sex == 1,])
fit_male <- plyr::arrange(generics::augment(fit_male), age)
}
if (nrow(tmp[tmp$sex == 2,])!=0)
{
fit_female <- loess(expression ~ age, data = tmp[tmp$sex == 2,])
fit_female <- plyr::arrange(generics::augment(fit_female), age)
}
g <- highchart() %>%
hc_chart(type = 'scatter'
, zoomType = 'xy'
, events = list(selection = SelectFunction)
)
if (nrow(tmp[tmp$sex == 1,])!=0)
{
g <- g%>%
hc_add_series(data = list_parse2(tmp[tmp$sex == 1, c("jittered_age", "expression")]),
showInLegend = TRUE, color = "cornflowerblue", name = "Male")
}
if (nrow(tmp[tmp$sex == 2,])!=0)
{
g <- g%>%
hc_add_series(data = list_parse2(tmp[tmp$sex == 2, c("jittered_age", "expression")]),
showInLegend = TRUE, color = "hotpink", name = "Female")
}
if (nrow(tmp[tmp$sex == 1,])!=0)
{
g <- g%>%
hc_add_series(data = list_parse2(data.frame(fit_male$age, fit_male$.fitted)),
type = "line", showInLegend = FALSE, color = "cornflowerblue")
}
if (nrow(tmp[tmp$sex == 2,])!=0)
{
g <- g%>%
hc_add_series(data = list_parse2(data.frame(fit_female$age, fit_female$.fitted)),
type = "line", showInLegend = FALSE, color = "hotpink")
}
g <- g%>%
hc_plotOptions(line = list(lineWidth = 7),
scatter = list(marker = list(radius = 5, symbol = "circle", fillOpacity = 0.4)),
series = list(allowPointSelect = TRUE,
events = list(click = ClickFunction),
marker = list(states = list(select = list(fillColor = "lightgrey", lineWidth = 1, radius = 6, lineColor = "black")))))
} else if (colored == "none" & shaped != "none")
{
tmp$condition <- donorCondition[match(tmp$samp_id, donorCondition$SAMPID), match(shaped, colnames(donorCondition))]
#Fitting of a regression per condition if the number of positive/negative case is higher than 10
if (length(which(tmp$condition %in% c(0,1))) == 0)
{
fit <- loess(expression ~ age, data = tmp)
fit <- plyr::arrange(generics::augment(fit), age)
g <- highchart() %>%
hc_chart(type = 'scatter') %>%
hc_add_series(data = list_parse2(tmp[!(tmp$condition %in% c(0, 1)), c("jittered_age", "expression")]), showInLegend = TRUE,
marker = list(radius = 5, symbol = "circle"), color = "grey", name = "Unknown") %>%
# hc_add_series(data = list_parse2(data.frame(fit$age, fit$.fitted - 2*fit$.se.fit, fit$.fitted + 2*fit$.se.fit)),
# type = "arearange", showInLegend = FALSE,
# color = "gainsboro", opacity = 0.005) %>%
hc_add_series(data = list_parse2(data.frame(fit$age, fit$.fitted)),
type = "line", showInLegend = FALSE,
lineWidth = 7, color = "black") %>%
hc_legend(title = list(text = shaped,
style = list(fontSize = '16px'))) %>%
hc_plotOptions(series = list(allowPointSelect = TRUE,
events = list(click = ClickFunction),
marker = list(states = list(select = list(fillColor = "lightgrey", lineWidth = 1, radius = 6, lineColor = "black")))))
}else if (min(table(tmp$condition)[names(table(tmp$condition)) %in% c(0,1)]) >= 10)
{
fit_positive <- loess(expression ~ age, data = tmp[tmp$condition == 1,])
fit_positive <- plyr::arrange(generics::augment(fit_positive), age)
fit_negative <- loess(expression ~ age, data = tmp[tmp$condition == 0,])
fit_negative <- plyr::arrange(generics::augment(fit_negative), age)
median_positive <- data.frame(20:70, rep(median(tmp$expression[which(tmp$condition == 1)]), length(20:70)))
median_negative <- data.frame(20:70, rep(median(tmp$expression[which(tmp$condition == 0)]), length(20:70)))
g <- highchart() %>%
hc_chart(type = 'scatter'
, zoomType = 'xy'
, events = list(selection = SelectFunction)
) %>%
hc_add_series(data = list_parse2(tmp[tmp$condition == 1, c("jittered_age", "expression")]), showInLegend = TRUE,
marker = list(radius = 7, symbol = "triangle"), color = "rgb(60,179,113)", name = "Positive") %>%
hc_add_series(data = list_parse2(tmp[tmp$condition == 0, c("jittered_age", "expression")]), showInLegend = TRUE,
marker = list(radius = 7, symbol = "cross"), color = "rgb(255,99,71)", name = "Negative") %>%
hc_add_series(data = list_parse2(tmp[!(tmp$condition %in% c(0, 1)), c("jittered_age", "expression")]), showInLegend = TRUE,
marker = list(radius = 5, symbol = "circle"), color = "grey", name = "Unknown") %>%
hc_add_series(data = list_parse2(data.frame(fit_positive$age, fit_positive$.fitted)),
type = "line", showInLegend = FALSE,
lineWidth = 7, color = "rgb(60,179,113)") %>%
hc_add_series(data = list_parse2(data.frame(fit_negative$age, fit_negative$.fitted)),
type = "line", showInLegend = FALSE,
lineWidth = 7, color = "rgb(255,99,71)") %>%
hc_add_series(data = list_parse2(median_positive), type = "line", name = "median - Positive",
marker = list(enabled = F),
color = "rgb(60,179,113)", dashStyle = "Dash") %>%
hc_add_series(data = list_parse2(median_negative), type = "line", name = "median - Negative",
marker = list(enabled = F),
color = "rgb(255,99,71)", dashStyle = "Dash") %>%
hc_legend(title = list(text = shaped,
style = list(fontSize = '16px'))) %>%
hc_plotOptions(series = list(allowPointSelect = TRUE,
events = list(click = ClickFunction),
marker = list(states = list(select = list(fillColor = "lightgrey", lineWidth = 1, radius = 6, lineColor = "black")))))
} else
{
fit <- loess(expression ~ age, data = tmp)
fit <- plyr::arrange(generics::augment(fit), age)
g <- highchart() %>%
hc_chart(type = 'scatter'
, zoomType = 'xy', events = list(selection = SelectFunction)
) %>%
hc_add_series(data = list_parse2(tmp[tmp$condition == 1, c("jittered_age", "expression")]), showInLegend = TRUE,
marker = list(radius = 7, symbol = "triangle"), color = "rgb(60,179,113)", name = "Positive") %>%
hc_add_series(data = list_parse2(tmp[tmp$condition == 0, c("jittered_age", "expression")]), showInLegend = TRUE,
marker = list(radius = 7, symbol = "cross"), color = "rgb(255,99,71)", name = "Negative") %>%
hc_add_series(data = list_parse2(tmp[!(tmp$condition %in% c(0, 1)), c("jittered_age", "expression")]), showInLegend = TRUE,
marker = list(radius = 5, symbol = "circle"), color = "grey", name = "Unknown") %>%
# hc_add_series(data = list_parse2(data.frame(fit$age, fit$.fitted - 2*fit$.se.fit, fit$.fitted + 2*fit$.se.fit)),
# type = "arearange", showInLegend = FALSE,
# color = "gainsboro", opacity = 0.005) %>%
hc_add_series(data = list_parse2(data.frame(fit$age, fit$.fitted)),
type = "line", showInLegend = FALSE,
lineWidth = 7, color = "black") %>%
hc_legend(title = list(text = shaped,
style = list(fontSize = '16px'))) %>%
hc_plotOptions(series = list(allowPointSelect = TRUE,
events = list(click = ClickFunction),
marker = list(states = list(select = list(fillColor = "lightgrey", lineWidth = 1, radius = 6, lineColor = "black")))))
}
} else if (colored == "Sex" & shaped != "none")
{
tmp$condition <- donorCondition[match(tmp$samp_id, donorCondition$SAMPID), match(shaped, colnames(donorCondition))]
if (nrow(tmp[tmp$sex == 1,])!=0)
{
fit_male <- loess(expression ~ age, data = tmp[tmp$sex == 1,])
fit_male <- plyr::arrange(generics::augment(fit_male), age)
}
if (nrow(tmp[tmp$sex == 2,])!=0)
{
fit_female <- loess(expression ~ age, data = tmp[tmp$sex == 2,])
fit_female <- plyr::arrange(generics::augment(fit_female), age)
}
g <- highchart() %>%
hc_chart(type = 'scatter'
, zoomType = 'xy', events = list(selection = SelectFunction))
#Male and conditions
if (nrow(tmp[tmp$sex == 1,])!=0)
{
g <- g %>%
hc_add_series(data = list_parse2(tmp[tmp$sex == 1 & tmp$condition == 1, c("jittered_age", "expression")]),
showInLegend = FALSE, color = "cornflowerblue", name = "Male - Pos",
marker = list(radius = 7, symbol = "triangle")) %>%
hc_add_series(data = list_parse2(tmp[tmp$sex == 1 & tmp$condition == 0, c("jittered_age", "expression")]),
showInLegend = FALSE, color = "cornflowerblue", name = "Male - Neg",
marker = list(radius = 7, symbol = "cross")) %>%
hc_add_series(data = list_parse2(tmp[tmp$sex == 1 & !(tmp$condition %in% c(0, 1)), c("jittered_age", "expression")]),
showInLegend = FALSE, color = "cornflowerblue", name = "Male - Unknown",
marker = list(radius = 5, symbol = "circle"))
}
if (nrow(tmp[tmp$sex == 2,])!=0)
{
g <- g %>%
#Female and conditions
hc_add_series(data = list_parse2(tmp[tmp$sex == 2 & tmp$condition == 1, c("jittered_age", "expression")]),
showInLegend = FALSE, color = "hotpink", name = "Female - Pos",
marker = list(radius = 7, symbol = "triangle")) %>%
hc_add_series(data = list_parse2(tmp[tmp$sex == 2 & tmp$condition == 0, c("jittered_age", "expression")]),
showInLegend = FALSE, color = "hotpink", name = "Female - Neg",
marker = list(radius = 7, symbol = "cross")) %>%
hc_add_series(data = list_parse2(tmp[tmp$sex == 2 & !(tmp$condition %in% c(0, 1)), c("jittered_age", "expression")]),
showInLegend = FALSE, color = "hotpink", name = "Female - Unknown",
marker = list(radius = 5, symbol = "circle"))
}
if (nrow(tmp[tmp$sex == 1,])!=0)
{
g <- g %>%
#Loess fitting for both sex
hc_add_series(data = list_parse2(data.frame(fit_male$age, fit_male$.fitted)),
type = "line", showInLegend = FALSE, color = "cornflowerblue", lineWidth = 7)
}
if (nrow(tmp[tmp$sex == 2,])!=0)
{
g <- g%>%
hc_add_series(data = list_parse2(data.frame(fit_female$age, fit_female$.fitted)),
type = "line", showInLegend = FALSE, color = "hotpink", lineWidth = 7)
}
g <- g%>%
#Fake series to create legend
hc_add_series(type = "scatter", name = "Positive", color= "grey",
marker = list(symbol = "triangle", radius = 8), showInLegend = TRUE) %>%
hc_add_series(type = "scatter", name = "Negative", color= "grey",
marker = list(symbol = "cross", radius = 8), showInLegend = TRUE) %>%
hc_add_series(type = "scatter", name = "Unknown", color= "grey",
marker = list(symbol = "circle", radius = 8), showInLegend = TRUE) %>%
hc_add_series(type = "scatter", name = "Male", color= "cornflowerblue",
marker = list(symbol = "circle", radius = 8), showInLegend = TRUE) %>%
hc_add_series(type = "scatter", name = "Female", color= "hotpink",
marker = list(symbol = "circle", radius = 8), showInLegend = TRUE) %>%
hc_legend(title = list(text = shaped,
style = list(fontSize = '16px'))) %>%
#Options for point click and selection
hc_plotOptions(series = list(allowPointSelect = TRUE,
events = list(click = ClickFunction),
marker = list(states = list(select = list(fillColor = "lightgrey", lineWidth = 1, radius = 6, lineColor = "black")))))
}
g <- g %>%
hc_xAxis(title = list(text = "Age (years)"), min = 20, max = 70) %>%
hc_yAxis(title = list(text = "Gene Expression (logCPM)")) %>%
hc_tooltip(formatter = JS("function(){return ' <b>GE</b>: ' + Highcharts.numberFormat(this.point.y, 2) + ' logCPM';}"), useHTML = TRUE) %>%
#hc_tooltip(formatter = JS("function(){return '<b>Age</b>: ' + this.point.x + ' y.o., <br><b>GE</b>: ' + Highcharts.numberFormat(this.point.y, 2) + ' logCPM';}"), useHTML = TRUE) %>%
#hc_title(text = gene) %>%
hc_subtitle(text = geneInfo)
return(g)
}
datatable_donorInfo <- function(geneData, tissue, selectedPoint, xmin, xmax, ymin, ymax, indexPoint, donorCondition, conditionID)
{
tmp <- geneData[geneData$tissue == tissue,]
tmp$sex[tmp$sex == 1] <- "M"
tmp$sex[tmp$sex == 2] <- "F"
if (selectedPoint == "hover" | selectedPoint == "") #one point selected
{
tmp <- tmp[indexPoint,]
} else if (is.numeric(xmin) | is.numeric(xmax) | is.numeric(ymin) | is.numeric(ymax))
{
tmp <- tmp[tmp$expression >= ymin & tmp$expression <= ymax & tmp$age >= xmin & tmp$age <= xmax,]
} else
{
tmp <- tmp
}
tmp <- cbind(tmp, donorCondition[match(tmp$samp_id, donorCondition$SAMPID), -1])
tmp[tmp == 1] <- as.character(tags$i(
class = "fa fa-check",
style = "color: rgb(60,179,113)"))
tmp[tmp == 0] <- as.character(tags$i(
class = "fa fa-times",
style = "color: rgb(255,99,71)"))
tmp[is.na(tmp)] <- as.character(tags$i(
class = "fa fa-question",
style = "color: rgb(169,169,169)"))
tmp[tmp == 96] <- as.character(tags$i(
class = "fa fa-question",
style = "color: rgb(169,169,169)"))
tmp[tmp == 97] <- as.character(tags$i(
class = "fa fa-question",
style = "color: rgb(169,169,169)"))
tmp[tmp == 99] <- as.character(tags$i(
class = "fa fa-question",
style = "color: rgb(169,169,169)"))
tmp <- tmp[, c("samp_id", "age", "expression", "sex", colnames(donorCondition)[-1])]
tmp$expression <- round(tmp$expression, 2)
tmp$age <- as.character(cut(tmp$age, breaks = seq(20,70, by = 5), include.lowest = T))
DT::datatable(tmp[, -which(colnames(tmp) == "samp_id")],
escape = F,
caption = htmltools::tags$caption(style = 'caption-side: top; text-align: center;',
'Positive: ',
tags$i(class = "fa fa-check", style = "color: rgb(60,179,113)"),
'- Negative: ',
tags$i(class = "fa fa-times", style = "color: rgb(255,99,71)"),
'- Unknown: ',
tags$i(class = "fa fa-question", style = "color: rgb(169,169,169)")
),
rownames = tmp$samp_id,
#extensions = 'Buttons', no integrated downlaod bttn
extensions = "FixedColumns", #freeze the 4 first columns
selection = "none",
colnames = c("Age interval (years)", "Gene Expression (logCPM)", "Sex",
# c("Cytomegalovirus", "EB Virus", "Hepatitis B 1.", "Hepatitis B 2.", "Hepatitis C", "Abnormal WBC", "Alzheimer's", "Arthritis", "Ascites", "Asthma", "Infections", "Past Blood Donations Denied",
# "Cancer 1.", "Cancer 2.", "Respiratory Disease 1.", "Cocaine", "Respiratory Disease 2.", "Cerebrovascular Disease", "Dialysis", "Dementia", "Depression", "Heart attack", "Ischemic Heart Disease",
# "Heart Disease", "Hypertension", "Liver disease", "Open wounds", "Transplant", "Osteomyelitis", "Pill abuse", "Pneumonia 1.", "Pneumonia 2.", "+ blood culture", "Rheumatoid Arthritis",
# "Renal Failure", "Schizophrenia", "Sepsis", "Steroid", "Seizures", "Diabetes I", "Diabetes II", "Toxics", "Loss weight")
as.character(conditionID$ID[match(colnames(donorCondition)[-1], conditionID$description)])
),
options = list(scrollX = T
, fixedColumns = list(leftColumns = 4) #freeze the 4 first columns
, autoWidth = TRUE
# ,
# columnDefs = list(list(targets = 0, render = JS(
# "function(data, type, row, meta) {",
# "return type === 'display' && data.length > 5 ?",
# "'<span title=\"' + data + '\">' + data.substr(0, 5) + '...</span>' : data;",
# "}")
# ))
),
callback = JS("var tips = ['GTEx sample ID',
'Age of the donor by quinquennium',
'Gene Expression in logCPM',
'Sex of the donor',
'Cytomegalovirus Total Antibody blood test',
'Epstein-Barr Virus IgG Antibody Blood test',
'Hepatitis B core Antibody IgM',
'Hepatitis B core Antibody Total',
'Hepatitis C virus Antibody testing',
'Abnormal White Blood Count',
'Alzheimers OR Dementia',
'Arthritis',
'Ascites',
'Asthma',
'Bacterial Infections (including septicemia (bacteria in the blood), meningococcal disease, staphylococcal infection, streptococcus, sepsis)',
'Past Blood Donations Denied',
'Cancer Diagnosis in the last 5y',
'History Of Non Metastatic Cancer',
'Chronic Lower Respiratory Disease',
'Cocaine Use In 5y',
'Chronic Respiratory Disease (Chronic Obstructive Pulmonary Syndrome (COPD) OR Chronic Lower Respiratory Disease (CLRD) (chronic bronchitis, emphysema, asthma))',
'Cerebrovascular Disease (stroke, TIA, embolism, aneurysm, other circulatory disorder affecting the brain)',
'Dialysis Treatment',
'Dementia With Unknown Cause',
'Major depression (unipolar depression, major depressive disorder)',
'Heart attack, acute myocardial infarction, acute coronary syndrome',
'Ischemic Heart Disease (coronary artery disease (CAD), coronary heart disease, ischemic cardiomyopathy)',
'Heart Disease',
'Hypertension',
'Liver Disease (liver abscess, failure, fatty liver syndrome, inherited liver insufficiency, acute/chronic hepatic insufficiency, necrobacillosis, rupture)',
'Open Wounds',
'Received Tissue Organ Transplant',
'Osteomyelitis',
'Prescription Pill Abuse',
'Pneumonia',
'Pneumonia (acute respiratory infection affecting the lungs)',
'Positive Blood Cultures',
'Rheumatoid Arthritis',
'Renal Failure',
'Schizophrenia',
'Documented Sepsis',
'Long Term Steroid Use',
'Unexplained Seizures',
'Diabetes mellitus type 1 (IDDM, formerly juvenile diabetes)',
'Diabetes mellitus type II (NIDDM, adult onset diabetes)',
'Exposure To Toxics',
'Unexplained Weight Loss (Information)'],
header = table.columns().header();
for (var i = 0; i < tips.length; i++) {$(header[i]).attr('title', tips[i]);}"),
) %>%
DT::formatStyle("sex", backgroundColor = DT::styleEqual(c("M", "F"), c('aliceblue', 'mistyrose')))
}
Heatmap_LoessGEvsAge <- function(data)
{
#a <- dbGetQuery(DBconnection, paste("SELECT * FROM", "A1BG_AS1", sep = " "))
a <- data
b <- data.frame()
for (k in unique(a$tissue))
{
fit <- a[a$tissue == k,]
fit <- loess(expression ~ age, data = fit)
b <- rbind(b, data.frame(age = 20:70, expression = predict(fit, 20:70), tissue = k))
}
b <- dcast(b, tissue~age, value.var = "expression")
rownames(b) <- b$tissue
b <- b[,-1]
b <- t(scale(t(b), scale = T))
i <- (hclust(dist(b)))
b <- b[i$order, ]
#b[is.na(b)] <- -100
b <- melt(b)
colnames(b) <- c("tissue", "age", "expression")
g <- hchart(b, type = "heatmap", hcaes(x = age, y = tissue, value = expression)) %>%
hc_colorAxis(stops = list(list(0.3, "dodgerblue"), list(0.5, "white"), list(0.7, "tomato")),
min = -2, max = 2,
reversed = F) %>%
hc_tooltip(formatter = JS("function(){if (!this.point.options.expression)
{return '<b>Age</b>: ' + this.point.age + ' y.o., <br><b>Tissue</b>: ' + this.point.tissue + ',<br><b>scaled GE </b>: No data'}
else
{return '<b>Age</b>: ' + this.point.age + ' y.o., <br><b>Tissue</b>: ' + this.point.tissue + ',<br><b>scaled GE</b>: ' + Highcharts.numberFormat(this.point.options.expression, 2);}
}")) %>%
hc_legend(title = list(text = "<center>Gene Expression<br>(Z-scores)</center>", style = list(fontSize = '16px')),align = "right", layout = "vertical", verticalAlign = "top",reversed = TRUE) %>%
hc_xAxis(title = list(text = "Age (years)", style = list(fontSize = '18px')),
labels = list(style = list(fontSize = "14px"))) %>%
hc_yAxis(title = list(text = "Tissue", style = list(fontSize = '18px')))
return(g)
}
Heatmap_NESAgevsPathway <- function(peak, tissue, variable, enrichment, Cluster_Reactome, ALL = TRUE)
{
if (ALL == TRUE)
{
#Pick pathwyas that are signifcant for the peak to reduce their number and make the plot more easily readable
temp <- peak[peak$tissue == tissue & peak$variable == variable,]
i <- enrichment$pathway[which(enrichment$padj <= 0.05
& enrichment$padj <= quantile(enrichment$padj, 0.01)
& enrichment$age %in% temp$age[temp$sig == "sig"])]
i <- unique(i)
while (identical(i, character(0))) #in some cases the previous filtering of intersting pathways reduces to 0 their number, so easing of the filtring
{
threshold <- 0.02
i <- enrichment$pathway[which(enrichment$padj <= 0.05
& enrichment$padj <= quantile(enrichment$padj, threshold)
& enrichment$age %in% temp$age[temp$sig == "sig"])]
i <- unique(i)
threshold <- threshold + 0.01
}
#Matrix of NES over time for selcted pathwas
i <- which(enrichment$pathway %in% i & enrichment$variable == variable)
tmp <- dcast(enrichment[i,], pathway ~ age, value.var = "NES")
rownames(tmp) <- tmp$pathway
tmp <- tmp[, -1]
tmp <- as.matrix(tmp[hclust(dist(tmp))$order,])
} else
{
tmp <- dcast(enrichment[enrichment$variable == variable,], pathway ~ age, value.var = "NES")
rownames(tmp) <- tmp$pathway
tmp <- tmp[, -1]
if (nrow(tmp) > 1)
{
tmp <- as.matrix(tmp[hclust(dist(tmp))$order,])
} else
{
tmp <- as.matrix(tmp)
}
}
#family of the selected pathways, l is created to add the family info the heatmapo
temp <- Cluster_Reactome$cluster[match(rownames(tmp), Cluster_Reactome$pathways)]
l <- list()
for (i in 1:length(temp))
{
l <- c(l, list(list(y = 1, x = (i-1), value = temp[i], color = color2()[temp[i]], categories = rownames(tmp)[i])))
}
#Data preparaiton for the plot
tmp <- melt(tmp)
colnames(tmp) <- c("pathway", "age", "NES")
g <- hchart(tmp, type = "heatmap", yAxis = 1,
hcaes(y = as.factor(age), x = pathway, value = NES),
tooltip = list(pointFormat = HTML("<b>Age</b>: {point.age} <br> <b>Pathway</b> {point.pathway} <br> <b>NES</b> {point.NES:.2f}"),
headerFormat = HTML(""))) %>%
hc_chart(zoomType = "x") %>%
hc_colorAxis(stops = list(list(0.1, "black"),
list(0.3, "dodgerblue"),
list(0.5, "white"),
list(0.7, "tomato"),
list(0.9, "black")),
min = -4, max = 4) %>%
hc_legend(title = list(text = "NES")) %>%
hc_add_series(data = l, type = "heatmap", showInLegend = F,
tooltip = list(pointFormat = HTML("<b>Family</b>: {point.value} <br> <b>Pathway</b> {point.categories}"),
headerFormat = HTML(""))) %>%
hc_yAxis_multiples(
list(height = "10%", categories = as.factor(c("Family")), labels = list(enabled = FALSE), title = list(text = "Family")),
list(showLastLabel = TRUE, opposite = TRUE, height = "90%", top = "10%", lineWidth = 1,
categories = floor(unique(tmp$age)),
labels = list(step = 10, enabled = F),
title = list(text = ""))
) %>%
hc_xAxis(labels = list(enabled = F), tickWidth = 0, title = list(text = "Reactome pathways"))
#adding of the percentage of the sig genes on the right side
temp <- peak[peak$tissue == tissue & peak$variable == variable,]
temp <- temp[, c("tissue", "age", "PercSigGene")]
names(temp) <- c("x", "y", "value")
g1 <- hchart(temp, type = "heatmap",
hcaes(x = x, y = as.character(y), value = value)) %>%
hc_yAxis(height = "74%", top = "8.5%", bottom = "17.5%",
opposite = T, labels = list(step = 10), categories = floor(temp$y),
title = list(text = "Age (years)"), offset = -120, lineWidth = 0) %>%
hc_xAxis(title = "", labels = list(enabled = F), tickWidth = 0, lineWidth = 0,
width = '30%', right = "70%") %>%
hc_colorAxis(stops = color_stops(10, rev(plasma(10))),
reversed = F) %>%
hc_legend(title = list(text = "% altered <br> genes", style = list(transform = "rotate(90deg)", fontWeight = "bold")),
align = "right", useHTML = T, floating = T,
layout = "vertical", verticalAlign = "top", x = -10) %>%
hc_tooltip(pointFormat = HTML("<b>%alt genes</b>: {point.value:.2f} <br><b>Age:</b> {point.yf} y.o."),
headerFormat = HTML(""))
return(manipulateWidget::combineWidgets(g, g1, ncol = 2, colsize = c(3,1)))
}
wordcloud_family <- function(Cluster_Reactome_affiliation, family)
{
#browser()
tmp <- c(Cluster_Reactome_affiliation[[family]]$REACTOME.pathways,Cluster_Reactome_affiliation[[family]]$KEGG.GO.pathways)
tmp <- tmp[!is.na(tmp)]
tmp <- gsub("REACTOME", "", tmp)
tmp <- gsub("GO", "", tmp)
tmp <- gsub("KEGG", "", tmp)
tmp <- gsub("_", " ", tmp)
# remove uninformative words
tmp <- gsub("PROCESS", "", tmp)
tmp <- gsub("REGULATION", "", tmp)
for (i in toupper(tm::stopwords("en")))
{
i <- paste0(" ", i, " ")
tmp <- gsub(i, " ", tmp)
}
tmp <- tm::VCorpus(tm::VectorSource(tmp))
tmp <- as.matrix(tm::TermDocumentMatrix(tmp))
tmp <- sort(rowSums(tmp), decreasing = T)
tmp <- data.frame(word = names(tmp), freq = tmp)
tmp$color <- rev(colorRampPalette(c("black", color2()[family]))(2*max(tmp$freq)))[tmp$freq]
if (max(tmp$freq) >= 3)
{
g <- hchart(tmp[tmp$freq >= 3,], "wordcloud",
hcaes(name = word, weight = freq, color = color), name = "Occurence") %>%
hc_title(text = paste("Family", family))
} else
{
g <- hchart(tmp[tmp$freq >= 2,], "wordcloud",
hcaes(name = word, weight = freq, color = color), name = "Occurence") %>%
hc_title(text = paste("Family", family))
}
return(g)
}
Heatmap_family <- function(Cluster_Reactome)
{
tmp <- data.frame(Family = 1:length(unique(Cluster_Reactome$cluster)))
tmp$color <- color2()[tmp$Family]
rownames(tmp) <- tmp$Family
l <- list()
for (i in 1:nrow(tmp))
{
l <- c(l, list(list(x = 1, y = (i-1), value = tmp$Family[i],
color = tmp$color[i], categories = tmp$Family[i])))
}
ClickFunction <- JS("function(event) {Shiny.onInputChange('familyClicked', event.point.categories) }")
ClickFunction2 <- JS("function(event) {console.log(event) }")
g <- highchart() %>%
hc_add_series(data = l, type = "heatmap", showInLegend = F,
tooltip = list(pointFormat = HTML("<b>Family</b>: {point.value}"),
headerFormat = HTML(""))) %>%
hc_yAxis(title = list(text = "Family"), tickAmount = length(unique(Cluster_Reactome$cluster)),
labels = list(formatter = JS("function(){return this.value+1;}"))) %>%
hc_xAxis(labels = list(enabled = FALSE), tickWidth = 0) %>%
hc_plotOptions(series = list(events = list(click = ClickFunction)))
return(g)
}
Heatmap_FisherTest_cellComposition <- function(pvalueFisherTest)
{
pvalueFisherTest$value <- round(pvalueFisherTest$value,2)
pvalueFisherTest$oddsRatio <- round(pvalueFisherTest$oddsRatio,2)
pvalueFisherTest$cellType <- gsub("\\.", " ", pvalueFisherTest$cellType)
names(pvalueFisherTest)[3] <- "value"
#Labls authrisation: when too many modules, difficult read yaxis laebls
legendLabels <- ifelse(length(unique(pvalueFisherTest$module)) <= 20, TRUE, FALSE)
pvalueFisherTest$tooltip_info <- with(pvalueFisherTest,
paste("<b>Module:</b> ", module,
"<br><b>Cell type:</b> ", cellType,
"<br><b>Odds Ratio:</b> ", oddsRatio,
"<br><b>-log<sub>10</sub>(p-value):</b> ", value))
# First, we ensure that the `value` column represents -log10(p-value)
# If it doesn't, you'll need to correct this.
# Create a new column for labeling based on the conditions you mentioned
pvalueFisherTest$label_value <- ifelse(pvalueFisherTest$oddsRatio > 1 & pvalueFisherTest$value > 1.3, pvalueFisherTest$oddsRatio, NA)
# Now, you simply check for the existence of this value in the labeling function
g <- hchart(pvalueFisherTest, type = "heatmap",
hcaes(x = cellType, y = module, value = oddsRatio)) %>%
hc_plotOptions(series = list(dataLabels = list(enabled = T,
formatter = JS("function(){if(!isNaN(this.point.label_value)){return this.point.label_value;}}")))) %>%
hc_legend(verticalAlign = "top", align = "left", layout = "vertical",
title = list(text = "Odds Ratio"), useHTML = TRUE) %>%
hc_colorAxis(stops = color_stops(9, RColorBrewer::brewer.pal(9, "Greens")),
min = 0, max = plyr::round_any(max(pvalueFisherTest$oddsRatio), 5, f = ceiling)) %>%
hc_tooltip(pointFormat = "{point.tooltip_info}", useHTML = T) %>%
hc_yAxis(labels = list(enabled = legendLabels), title = list(text = "Modules"),
lineWidth = 0, minorGridLineWidth = 0, gridLineWidth = 0) %>%
hc_xAxis(title = list(text = "Cell type"), labels = list(autoRotation = F, rotation = 60)) # Add the rotation argument here
return(g)
# #Adding of heatmap to depict the modules
# tmp <- data.frame(Module = levels(as.factor(pvalueFisherTest$module)))
# tmp$color <- gsub("ME", "", tmp$Module)
#
# #Since highcharter do not recognize all the color name, convert them to HEX odes
# colorHEX <- data.frame(color=colors(), HEX = rgb(t(col2rgb(colors())), maxColorValue=255), stringsAsFactors=FALSE)
#
# tmp$color <- colorHEX$HEX[match(tmp$color, colorHEX$color)]
# rownames(tmp) <- tmp$Module
#
# l <- list()
# for (i in 1:nrow(tmp))
# {
# l <- c(l, list(list(x = 1, y = (i-1), value = tmp$Module[i],
# color = tmp$color[i], categories = gsub(".*_", "", tmp$Module[i]))))
# }
#
#
# g1 <- highchart() %>%
# hc_add_series(data = l, type = "heatmap", showInLegend = F,
# tooltip = list(pointFormat = HTML("<b>Module</b>: {point.categories}"),
# headerFormat = HTML(""))) %>%
# hc_yAxis(height = paste0(95 - as.numeric(round(predict(fit, data.frame(x = nrow(tmp))), 2)), "%"), #fit used here
# top = paste0(round(predict(fit, data.frame(x = nrow(tmp))), 2), "%"), bottom = "5%",
# title = list(text = "Modules"), lineWidth = 0,
# minorGridLineWidth = 0, gridLineWidth = 0,
# opposite = T,
# labels = list(enabled = FALSE)) %>%
# hc_xAxis(labels = list(enabled = FALSE), tickWidth = 0, lineWidth = 0)