Makes barplots from RunEnrichr output.
Usage
EnrichrBarPlot(
seurat_obj,
outdir = "enrichr_plots",
n_terms = 25,
plot_size = c(6, 15),
logscale = FALSE,
plot_bar_color = NULL,
plot_text_color = NULL,
wgcna_name = NULL,
...
)Arguments
- seurat_obj
A Seurat object
- outdir
directory to place output .pdf files
- n_terms
the number of terms to plot in each barplot
- plot_size
the size of the output .pdf files (width, height)
- logscale
logical controlling whether to plot the enrichment on a log scale
- plot_bar_color
The color of the bars in the bar plots. Default option (NULL) makes the bars colored using the module's assigned color.
- plot_text_color
The color of the text labels on the bar plots
- wgcna_name
The name of the hdWGCNA experiment in the seurat_obj@misc slot
Examples
EnrichrBarPlot
#> function (seurat_obj, outdir = "enrichr_plots", n_terms = 25,
#> plot_size = c(6, 15), logscale = FALSE, plot_bar_color = NULL,
#> plot_text_color = NULL, wgcna_name = NULL, ...)
#> {
#> if (is.null(wgcna_name)) {
#> wgcna_name <- seurat_obj@misc$active_wgcna
#> }
#> modules <- GetModules(seurat_obj, wgcna_name)
#> mods <- levels(modules$module)
#> mods <- mods[mods != "grey"]
#> enrichr_df <- GetEnrichrTable(seurat_obj, wgcna_name)
#> wrapText <- function(x, len) {
#> sapply(x, function(y) paste(strwrap(y, len), collapse = "\n"),
#> USE.NAMES = FALSE)
#> }
#> if (!dir.exists(outdir)) {
#> dir.create(outdir)
#> }
#> for (i in 1:length(mods)) {
#> cur_mod <- mods[i]
#> cur_terms <- subset(enrichr_df, module == cur_mod)
#> print(cur_mod)
#> cur_color <- modules %>% subset(module == cur_mod) %>%
#> .$color %>% unique %>% as.character
#> if (!is.null(plot_bar_color)) {
#> cur_color <- plot_bar_color
#> }
#> if (nrow(cur_terms) == 0) {
#> next
#> }
#> cur_terms$wrap <- wrapText(cur_terms$Term, 45)
#> plot_list <- list()
#> for (cur_db in dbs) {
#> plot_df <- subset(cur_terms, db == cur_db) %>% top_n(n_terms,
#> wt = Combined.Score)
#> if (is.null(plot_text_color)) {
#> if (cur_color == "black") {
#> text_color = "grey"
#> }
#> else {
#> text_color = "black"
#> }
#> }
#> else {
#> text_color <- plot_text_color
#> }
#> if (logscale) {
#> plot_df$Combined.Score <- log(plot_df$Combined.Score)
#> lab <- "Enrichment log(combined score)"
#> x <- 0.2
#> }
#> else {
#> lab <- "Enrichment (combined score)"
#> x <- 5
#> }
#> plot_list[[cur_db]] <- ggplot(plot_df, aes(x = Combined.Score,
#> y = reorder(wrap, Combined.Score))) + geom_bar(stat = "identity",
#> position = "identity", color = "white", fill = cur_color) +
#> geom_text(aes(label = wrap), x = x, color = text_color,
#> size = 3.5, hjust = "left") + ylab("Term") +
#> xlab(lab) + ggtitle(cur_db) + theme(panel.grid.major = element_blank(),
#> panel.grid.minor = element_blank(), legend.title = element_blank(),
#> axis.ticks.y = element_blank(), axis.text.y = element_blank(),
#> plot.title = element_text(hjust = 0.5))
#> }
#> pdf(paste0(outdir, "/", cur_mod, ".pdf"), width = plot_size[1],
#> height = plot_size[2])
#> for (plot in plot_list) {
#> print(plot)
#> }
#> dev.off()
#> }
#> }
#> <bytecode: 0x7f962fdbb2d0>
#> <environment: namespace:hdWGCNA>