Makes barplots from Enrichr data
Usage
EnrichrDotPlot(
seurat_obj,
database,
mods = "all",
n_terms = 3,
break_ties = TRUE,
logscale = TRUE,
wgcna_name = NULL,
...
)Arguments
- seurat_obj
A Seurat object
- database
name of the enrichr database to plot.
- mods
names of modules to plot. All modules are plotted if mods='all' (default)
- n_terms
number of enriched terms to plot for each module
- break_ties
logical controlling whether or not to randomly select terms with equal enrichments to precisely enforce n_terms.
- logscale
logical controlling whether to plot the enrichment on a log scale.
- wgcna_name
The name of the hdWGCNA experiment in the seurat_obj@misc slot
Examples
EnrichrDotPlot
#> function (seurat_obj, database, mods = "all", n_terms = 3, break_ties = TRUE,
#> logscale = TRUE, wgcna_name = NULL, ...)
#> {
#> if (is.null(wgcna_name)) {
#> wgcna_name <- seurat_obj@misc$active_wgcna
#> }
#> modules <- GetModules(seurat_obj, wgcna_name)
#> if (mods == "all") {
#> mods <- levels(modules$module)
#> mods <- mods[mods != "grey"]
#> }
#> enrichr_df <- GetEnrichrTable(seurat_obj, wgcna_name)
#> mod_colors <- dplyr::select(modules, c(module, color)) %>%
#> dplyr::distinct()
#> enrichr_df$color <- mod_colors[match(enrichr_df$module, mod_colors$module),
#> "color"]
#> wrapText <- function(x, len) {
#> sapply(x, function(y) paste(strwrap(y, len), collapse = "\n"),
#> USE.NAMES = FALSE)
#> }
#> plot_df <- enrichr_df %>% subset(db == database & module %in%
#> mods) %>% group_by(module) %>% top_n(n_terms, wt = Combined.Score)
#> if (break_ties) {
#> plot_df <- do.call(rbind, lapply(plot_df %>% group_by(module) %>%
#> group_split, function(x) {
#> x[sample(n_terms), ]
#> }))
#> }
#> plot_df$Term <- wrapText(plot_df$Term, 45)
#> plot_df$module <- factor(as.character(plot_df$module), levels = levels(modules$module))
#> plot_df <- arrange(plot_df, module)
#> plot_df$Term <- factor(as.character(plot_df$Term), levels = unique(as.character(plot_df$Term)))
#> if (logscale) {
#> plot_df$Combined.Score <- log(plot_df$Combined.Score)
#> lab <- "Enrichment\nlog(combined score)"
#> x <- 0.2
#> }
#> else {
#> lab <- "Enrichment\n(combined score)"
#> x <- 5
#> }
#> p <- plot_df %>% ggplot(aes(x = module, y = Term)) + geom_point(aes(size = Combined.Score),
#> color = plot_df$color) + RotatedAxis() + ylab("") + xlab("") +
#> labs(size = lab) + scale_y_discrete(limits = rev) + ggtitle(database) +
#> theme(plot.title = element_text(hjust = 0.5), axis.line.x = element_blank(),
#> axis.line.y = element_blank(), panel.border = element_rect(colour = "black",
#> fill = NA, size = 1))
#> p
#> }
#> <bytecode: 0x7f96312257b8>
#> <environment: namespace:hdWGCNA>