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DiffBrainNet/04_PlotsManuscript/05_FigureIV_Bbase.R
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################################################## | |
## Project: DexStim Mouse Brain | |
## Date: 29.11.2021 | |
## Author: Nathalie | |
################################################## | |
# GO enrichment plot for manuscript | |
# Tcf4 baseline network in PFC | |
library(readxl) | |
library(dplyr) | |
library(stringr) | |
library(ggpubr) | |
# 1. GO enrichment for vCA unique DE genes and their diff neighbours | |
data <- read_xlsx(path = "~/Documents/ownCloud/DexStim_RNAseq_Mouse/manuscript/Figures/Figure IV_GWAS/TCF4/FUMA_baselin Tcf4PFCnetwork_gene2func68958/FUMA Tcf4BaselinePFCnetwork.xlsx", | |
sheet = "GO bp") | |
data <- arrange(data, desc(`[-log10]`)) | |
data <- data[1:25,] | |
# remove the "GO_" from GO terms | |
data$GeneSet <- str_replace_all(data$GeneSet, '^GO_', ' ') | |
# remove the "_" from GO terms | |
data$GeneSet <- str_replace_all(data$GeneSet, "_", " ") | |
# only capitalize first letter per word | |
data$GeneSet <- str_to_title(data$GeneSet) | |
# of and to should start with lower case | |
data$GeneSet <- str_replace_all(data$GeneSet, "Of", "of") | |
data$GeneSet <- str_replace_all(data$GeneSet, "To", "to") | |
data$GeneSet <- str_replace_all(data$GeneSet, " In ", " in ") | |
data$GeneSet <- str_replace_all(data$GeneSet, " Into ", " into ") | |
# make some terms shorter with abbreviations | |
data$GeneSet <- str_replace_all(data$GeneSet, "Positive Regulation", "Pos. Reg.") | |
data$GeneSet <- str_replace_all(data$GeneSet, "Negative Regulation", "Neg. Reg.") | |
# Ii from "Polymerase II" back to upper case | |
data$GeneSet <- str_replace_all(data$GeneSet, "Ii", "II") | |
# 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(1.9,1,1)) | |
ggexport(comb, filename = "05_FigureIV_Bbase.pdf", width = 14, height = 10) | |