Plots the results from OverlapModulesDEGs as a bar plot
Usage
OverlapBarPlot(
overlap_df,
plot_var = "odds_ratio",
logscale = FALSE,
neglog = FALSE,
label_size = 2,
...
)Arguments
- overlap_df
the Module/DEG overlap table from OverlapModulesDEGs
- plot_var
the name of the overlap statistic to plot
- logscale
logical controlling whether to plot the result on a log scale, useful for odds ratio
- neglog
logical controlling wehether to plot the result as a negative log, useful for p-value / FDR
- label_size
the size of the module labels in the bar plot
Examples
OverlapBarPlot
#> function (overlap_df, plot_var = "odds_ratio", logscale = FALSE,
#> neglog = FALSE, label_size = 2, ...)
#> {
#> label <- plot_var
#> if (plot_var == "odds_ratio") {
#> yint <- 1
#> }
#> else if (plot_var == "fdr") {
#> yint <- 0.05
#> }
#> if (logscale) {
#> overlap_df[[plot_var]] <- log(overlap_df[[plot_var]])
#> label <- paste0("log(", plot_var, ")")
#> yint = log(yint)
#> }
#> if (neglog) {
#> overlap_df[[plot_var]] <- -1 * log(overlap_df[[plot_var]])
#> label <- paste0("-log(", label, ")")
#> yint = -1 * log(yint)
#> }
#> groups <- overlap_df$group %>% as.character %>% unique
#> plot_list <- list()
#> for (cur_group in groups) {
#> cur_df <- overlap_df %>% subset(group == cur_group)
#> p <- cur_df %>% ggplot(aes(x = reorder(module, get(plot_var)),
#> y = get(plot_var))) + geom_bar(stat = "identity",
#> fill = cur_df$color) + coord_flip() + xlab("") +
#> ylab(label) + ggtitle(cur_group) + theme(axis.line.y = element_blank(),
#> axis.ticks.y = element_blank(), axis.text.y = element_blank(),
#> plot.title = element_text(hjust = 0.5))
#> if (plot_var == "fdr" | plot_var == "odds_ratio") {
#> p <- p + geom_hline(yintercept = yint, linetype = "dashed",
#> color = "gray")
#> }
#> p <- p + geom_text(aes(label = module, x = module, y = get(plot_var)),
#> color = "black", size = label_size, hjust = "inward")
#> plot_list[[cur_group]] <- p
#> }
#> plot_list
#> }
#> <bytecode: 0x7f96347622a8>
#> <environment: namespace:hdWGCNA>