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DiffBrainNet/04_PlotsManuscript/14_FigureSIV_gwas.R
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################################################## | |
## Project: DexStim Mouse Brain | |
## Date: 30.11.2021 | |
## Author: Nathalie | |
################################################## | |
# GWAS enrichment plot for manuscript | |
# Tcf4 neighbours? | |
library(readxl) | |
library(dplyr) | |
library(ggplot2) | |
library(ggpubr) | |
# 1. Pathway enrichment for Abcd1 and neighbours | |
data <- read_xlsx(path = "~/Documents/ownCloud/DexStim_RNAseq_Mouse/manuscript/Figures/Figure IV_GWAS/TCF4/FUMA_diffTcf4PFCnetwork_gene2func68788/FUMA_diffPFCTcf4.xlsx", | |
sheet = "GWAS") | |
data <- arrange(data, desc(`[-log10]`)) | |
data$`my adj p` <- as.numeric(data$`my adj p`) | |
data <- data[data$`my adj p` <= 0.05,] | |
data <- data[!is.na(data$`my adj p`),] | |
# GeneSet as factor | |
data$GeneSet <- factor(data$GeneSet, levels = data$GeneSet) | |
# bar plot gene ratio | |
gr <- ggplot(data, aes(x = GeneSet, y = `Genes ratio`) ) + | |
geom_bar(position = position_dodge2(reverse=TRUE), stat="identity", fill = "#0F5057") + | |
scale_fill_manual() + | |
theme_light() + | |
coord_flip() + | |
scale_x_discrete(limits = rev) + | |
theme(text = element_text(size= 14)) + | |
ylab("% Gene Ratio") + | |
labs(x = NULL) | |
# bar plot odds ratio | |
or <- ggplot(data, aes(x = GeneSet, y = `OR[log2(a*d)-log2(b*c)]`) ) + | |
geom_bar(position = position_dodge2(reverse=TRUE), stat="identity", fill = "#FAA916") + | |
scale_fill_manual() + | |
theme_light() + | |
coord_flip() + | |
scale_x_discrete(limits = rev) + | |
theme(text = element_text(size= 14)) + | |
ylab("Odds Ratio") + | |
labs(x = NULL) | |
# barplot fdr p-value | |
fdr <- ggplot(data, aes(x = GeneSet, y = `[-log10]`) ) + | |
geom_bar(position = position_dodge2(reverse=TRUE), stat="identity", fill = "#D45E60") + | |
geom_hline(yintercept = -log10(0.05),linetype="dashed", color = "red") + | |
theme_light() + | |
coord_flip() + | |
scale_x_discrete(limits = rev) + | |
theme(text = element_text(size= 14)) + | |
ylab("-log10(FDR)") + | |
labs(x = NULL) | |
# combined barplot | |
comb <- ggarrange(gr, | |
or + | |
theme(axis.text.y = element_blank(), | |
axis.ticks.y = element_blank(), | |
axis.title.y = element_blank() ), | |
fdr + | |
theme(axis.text.y = element_blank(), | |
axis.ticks.y = element_blank(), | |
axis.title.y = element_blank() ), | |
nrow = 1, | |
widths = c(1.8,1,1)) | |
ggexport(comb, filename = "14_FigureSIV_gwas.pdf", width = 14, height = 8) | |