Plots of WGCNA Module Over-Representation Analysis Results

Tyler Sagendorf

01 May, 2024

This article generates plots of the WGCNA over-representation analysis results (Fig. 4C–E).

library(MotrpacRatTraining6moWATData)
library(MotrpacRatTraining6moWAT) # plot_ORA
library(dplyr)
library(ggplot2)

save_plots <- dir.exists(paths = file.path("..", "..", "plots"))

METAB

METAB_MODULE_ORA <- mutate(METAB_MODULE_ORA,
                           gs_subcat = "refmet_sub_class",
                           pathway = refmet_sub_class,
                           gs_description = refmet_sub_class)

p_metab <- plot_ORA(METAB_MODULE_ORA,
                    mods = 1:7,
                    subset = "refmet_sub_class")

ggsave(file.path("..", "..", "plots", "METAB_module_ORA_dotplot.pdf"), p_metab,
       height = 1.8, width = 2.2, family = "ArialMT")

PROT

## MF
prot_MF <- plot_ORA(PROT_MODULE_ORA,
                    subset = "GO:MF",
                    mods = 1:11,
                    rel_heights = c(0.8, 0.1))

ggsave(file.path("..", "..", "plots", "PROT_module_ORA_GO-MF_dotplot.pdf"), prot_MF,
       height = 3, width = 3, family = "ArialMT")

## BP
prot_BP <- plot_ORA(PROT_MODULE_ORA,
                    subset = "GO:BP",
                    mods = 1:11,
                    rel_heights = c(0.8, 0.1))

ggsave(file.path("..", "..", "plots", "PROT_module_ORA_GO-BP_dotplot.pdf"), prot_BP,
       height = 3, width = 3, family = "ArialMT")

## CC
prot_CC <- plot_ORA(PROT_MODULE_ORA,
                    subset = "GO:CC",
                    mods = 1:11,
                    rel_heights = c(0.8, 0.1))

ggsave(file.path("..", "..", "plots", "PROT_module_ORA_GO-CC_dotplot.pdf"), prot_CC,
       height = 3, width = 3, family = "ArialMT")

TRNSCRPT

# MF
trnscrpt_MF <- plot_ORA(TRNSCRPT_MODULE_ORA,
                        subset = "GO:MF",
                        mods = 1:14,
                        n_terms = 4,
                        rel_heights = c(1, 0.15))

ggsave(file.path("..", "..", "plots", "TRNSCRPT_module_ORA_GO-MF_dotplot.pdf"), trnscrpt_MF,
       height = 4, width = 3.5, family = "ArialMT")

# BP
trnscrpt_BP <- plot_ORA(TRNSCRPT_MODULE_ORA,
                        subset = "GO:BP",
                        mods = 1:14,
                        n_terms = 4,
                        rel_heights = c(1, 0.09))

ggsave(file.path("..", "..", "plots", "TRNSCRPT_module_ORA_GO-BP_dotplot.pdf"), trnscrpt_BP,
       height = 5, width = 3.5, family = "ArialMT")

# CC
trnscrpt_CC <- plot_ORA(TRNSCRPT_MODULE_ORA,
                        subset = "GO:CC",
                        mods = 1:14, n_terms = 4,
                        rel_heights = c(1, 0.15))

ggsave(file.path("..", "..", "plots", "TRNSCRPT_module_ORA_GO-CC_dotplot.pdf"), trnscrpt_CC,
       height = 4, width = 3.5, family = "ArialMT")