PlotDMEsVolcano

Plotting function for the results of FindDMEs and FindAllDMEs

PlotDMEsVolcano(
  seurat_obj,
  DMEs,
  plot_labels = TRUE,
  mod_point_size = 4,
  label_size = 4,
  show_cutoff = TRUE,
  wgcna_name = NULL
)

Arguments

DMEs

dataframe output from FindDMEs or FindAllDMEs

plot_labels

logical determining whether to plot the module labels

mod_point_size

the size of the points in each plot

label_size

the size of the module labels

show_cutoff

logical determining whether to plot the significance cutoff. Should set this to FALSE if using facet_wrap.

wgcna_name

The name of the hdWGCNA experiment in the seurat_obj@misc slot

Value

A ggplot object

Examples

PlotDMEsVolcano
#> function (seurat_obj, DMEs, plot_labels = TRUE, mod_point_size = 4, 
#>     label_size = 4, show_cutoff = TRUE, wgcna_name = NULL) 
#> {
#>     if (is.null(wgcna_name)) {
#>         wgcna_name <- seurat_obj@misc$active_wgcna
#>     }
#>     DMEs <- na.omit(DMEs)
#>     lowest <- DMEs %>% subset(p_val_adj != 0) %>% top_n(-1, wt = p_val_adj) %>% 
#>         .$p_val_adj
#>     DMEs$p_val_adj <- ifelse(DMEs$p_val_adj == 0, lowest, DMEs$p_val_adj)
#>     max_fc <- max(abs(DMEs$avg_log2FC))
#>     max_fc <- DMEs %>% subset(abs(avg_log2FC) != Inf) %>% .$avg_log2FC %>% 
#>         max
#>     DMEs$avg_log2FC <- ifelse(DMEs$avg_log2FC == -Inf, -1 * max_fc, 
#>         DMEs$avg_log2FC)
#>     DMEs$avg_log2FC <- ifelse(DMEs$avg_log2FC == Inf, max_fc, 
#>         DMEs$avg_log2FC)
#>     modules <- GetModules(seurat_obj, wgcna_name) %>% subset(module != 
#>         "grey") %>% mutate(module = droplevels(module))
#>     module_colors <- modules %>% dplyr::select(c(module, color)) %>% 
#>         distinct
#>     mods <- levels(modules$module)
#>     mods <- mods[mods %in% DMEs$module]
#>     mod_colors <- module_colors$color
#>     names(mod_colors) <- as.character(module_colors$module)
#>     DMEs$anno <- ifelse(DMEs$p_val_adj < 0.05, DMEs$module, "")
#>     xmax <- max_fc
#>     p <- DMEs %>% ggplot(aes(x = avg_log2FC, y = -log10(p_val_adj), 
#>         fill = module, color = module))
#>     if (show_cutoff) {
#>         p <- p + geom_vline(xintercept = 0, linetype = "dashed", 
#>             color = "grey75", alpha = 0.8) + geom_rect(data = DMEs[1, 
#>             ], aes(xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = -log10(0.05)), 
#>             fill = "grey75", alpha = 0.8, color = NA)
#>     }
#>     p <- p + geom_point(size = mod_point_size, pch = 21, color = "black")
#>     if (plot_labels) {
#>         p <- p + ggrepel::geom_text_repel(aes(label = anno), 
#>             color = "black", min.segment.length = 0, max.overlaps = Inf, 
#>             size = label_size)
#>     }
#>     p <- p + scale_fill_manual(values = mod_colors) + scale_color_manual(values = mod_colors) + 
#>         xlim((-1 * xmax) - 0.1, xmax + 0.1) + xlab(bquote("Average log"[2] ~ 
#>         "(Fold Change)")) + ylab(bquote("-log"[10] ~ "(Adj. P-value)")) + 
#>         theme(panel.border = element_rect(color = "black", fill = NA, 
#>             size = 1), panel.grid.major = element_blank(), axis.line = element_blank(), 
#>             plot.title = element_text(hjust = 0.5), legend.position = "bottom") + 
#>         NoLegend()
#>     p + NoLegend()
#> }
#> <bytecode: 0x7f77d3d56268>
#> <environment: namespace:hdWGCNA>