Plot module eigengenes as a FeaturePlot
Usage
ModuleFeaturePlot(
seurat_obj,
module_names = NULL,
wgcna_name = NULL,
reduction = "umap",
features = "hMEs",
order_points = TRUE,
restrict_range = TRUE,
point_size = 0.5,
alpha = 1,
label_legend = FALSE,
ucell = FALSE,
raster = FALSE,
raster_dpi = 500,
raster_scale = 1,
plot_ratio = 1,
title = TRUE
)Examples
ModuleFeaturePlot
#> function (seurat_obj, module_names = NULL, wgcna_name = NULL,
#> reduction = "umap", features = "hMEs", order_points = TRUE,
#> restrict_range = TRUE, point_size = 0.5, alpha = 1, label_legend = FALSE,
#> ucell = FALSE, raster = FALSE, raster_dpi = 500, raster_scale = 1,
#> plot_ratio = 1, title = TRUE)
#> {
#> if (is.null(wgcna_name)) {
#> wgcna_name <- seurat_obj@misc$active_wgcna
#> }
#> if (features == "hMEs") {
#> MEs <- GetMEs(seurat_obj, TRUE, wgcna_name)
#> }
#> else if (features == "MEs") {
#> MEs <- GetMEs(seurat_obj, FALSE, wgcna_name)
#> }
#> else if (features == "scores") {
#> MEs <- GetModuleScores(seurat_obj, wgcna_name)
#> }
#> else if (features == "average") {
#> MEs <- GetAvgModuleExpr(seurat_obj, wgcna_name)
#> restrict_range <- FALSE
#> }
#> else (stop("Invalid feature selection. Valid choices: hMEs, MEs, scores, average"))
#> if (ucell) {
#> restrict_range <- FALSE
#> }
#> modules <- GetModules(seurat_obj, wgcna_name)
#> if (is.null(module_names)) {
#> module_names <- levels(modules$module)
#> module_names <- module_names[module_names != "grey"]
#> }
#> umap <- seurat_obj@reductions[[reduction]]@cell.embeddings
#> x_name <- colnames(umap)[1]
#> y_name <- colnames(umap)[2]
#> plot_df <- cbind(umap, MEs) %>% as.data.frame()
#> plot_list <- list()
#> for (cur_mod in module_names) {
#> print(cur_mod)
#> cur_color <- modules %>% subset(module == cur_mod) %>%
#> .$color %>% unique
#> plot_range <- plot_df[, cur_mod] %>% range
#> if (restrict_range) {
#> if (abs(plot_range[1]) > abs(plot_range[2])) {
#> plot_range[1] <- -1 * plot_range[2]
#> }
#> else {
#> plot_range[2] <- -1 * plot_range[1]
#> }
#> plot_df[, cur_mod] <- ifelse(plot_df[, cur_mod] >
#> plot_range[2], plot_range[2], plot_df[, cur_mod])
#> plot_df[, cur_mod] <- ifelse(plot_df[, cur_mod] <
#> plot_range[1], plot_range[1], plot_df[, cur_mod])
#> }
#> cur_plot_df <- plot_df[, c(colnames(umap), cur_mod)]
#> colnames(cur_plot_df)[3] <- "val"
#> if (order_points == TRUE) {
#> cur_plot_df <- cur_plot_df %>% dplyr::arrange(val)
#> }
#> else if (order_points == "shuffle") {
#> cur_plot_df <- cur_plot_df[sample(nrow(cur_plot_df)),
#> ]
#> }
#> p <- cur_plot_df %>% ggplot(aes_string(x = x_name, y = y_name,
#> color = "val"))
#> if (raster) {
#> p <- p + ggrastr::rasterise(geom_point(size = point_size,
#> alpha = alpha), dpi = raster_dpi, scale = raster_scale)
#> }
#> else {
#> p <- p + geom_point(size = point_size, alpha = alpha)
#> }
#> p <- p + umap_theme() + labs(color = "")
#> if (title) {
#> p <- p + ggtitle(cur_mod)
#> }
#> if (is.numeric(plot_ratio)) {
#> p <- p + coord_fixed(ratio = plot_ratio)
#> }
#> if (!ucell) {
#> p <- p + scale_color_gradient2(low = "grey75", mid = "grey95",
#> high = cur_color, breaks = plot_range, labels = c("-",
#> "+"), guide = guide_colorbar(ticks = FALSE,
#> barwidth = 0.5, barheight = 4))
#> }
#> else {
#> p <- p + scale_color_gradient(low = "grey95", high = cur_color,
#> breaks = plot_range, labels = c("0", "+"), guide = guide_colorbar(ticks = FALSE,
#> barwidth = 0.5, barheight = 4))
#> }
#> plot_list[[cur_mod]] <- p
#> }
#> if (length(plot_list) == 1) {
#> p <- plot_list[[1]]
#> }
#> else {
#> p <- plot_list
#> }
#> p
#> }
#> <bytecode: 0x7f9629c4e8e8>
#> <environment: namespace:hdWGCNA>