EDF7.R

# =======================================================================================================
# This is a script for generating EDF7: Allele specific expression across rare disease samples
#
# Note that the final figure was generated by using inkscape by combining figures from this script for visualization purposes
#
# =======================================================================================================



#!/bin/R


library(data.table)
library(dplyr)
library(ggplot2)
library(gridExtra)
library(reshape2)
library(cowplot)
library(ggrepel)
library(readr)
library(ggpubr)


fsize=15
RD_theme=theme_classic()+
    theme(axis.text.x= element_text(size=fsize),
    axis.text.y= element_text(size=fsize), 
    axis.title = element_text(size = fsize), 
    legend.text = element_text(size = fsize-1), 
    legend.title = element_text(size = fsize), 
    axis.ticks = element_line(size = 0.1),
    strip.background=element_blank(),
    panel.grid.major=element_blank(),
    panel.grid.minor=element_blank(),
    axis.text=element_text(size=9),

# Read in data
edf7a=read.table("EDF7a_data.txt", sep="\t", header=T)
edf7b=read.table("EDF7B_data.txt", sep="\t", header=T)



# EDF7A
color_variant=c( "#2F4E6F", "#98B1C4", "#C8D7E3")

edf7a_plot = ggplot(edf7a, aes(x=factor(variable), y=as.numeric(value), Group=variant_data)) +
geom_boxplot(aes(fill=variant_data)) + xlab('') +
ylab('Number per sample') +
RD_theme+ scale_fill_manual(values=color_variant,name="Variant data")+
scale_y_log10()+
theme(legend.position=c(0.8,0.9))+
scale_x_discrete(labels=c("allhets" = "Heterozygous\nsites",  "AI.65"="Allelic ratio\nover 0.65" ))

# EDF7B
cat.colors = c('grey', '#DEADA1')

edf7b_plot=ggplot(edf7b, aes(x=Filter,y=NumMatch, fill=Category)) + geom_boxplot(outlier.colour = NULL) + 
stat_compare_means(aes(group=Category),label =  "p.signif") +
scale_fill_manual(values=cat.colors)