EDF6.R

# =======================================================================================================
# This is a script for generating EDF6: Correction for batch effects - Splicing data
#
# Note that the final figure was generated by using inkscape by combining figures from this script for visualization purposes
#
# =======================================================================================================




#!/bin/R

#  Read in input data
edf6c=read.table("EDF6c_data.txt", sep="\t", header=T)

#Libraries
library(ggplot2)
library(cowplot)
library(ggpubr)

## Panel A

# PCA plot of first 2 PCs uncorrected data. PC1 and PC2 data available

## Panel B
# PCA plot of first 2 PCs corrected data. PC1 and PC2 data available

# Panel C
edf6c_plot=ggplot(data = edf6c, aes(x=Var2, y=as.factor(Var1), fill=value)) + 
  geom_tile(color = "white")+
 scale_fill_gradient2(low = "blue", high = "red", mid = "white", 
   midpoint = 0, limit = c(-1,1), space = "Lab", 
   name="Pearson\nCorrelation") +
  theme_minimal()+ 
  coord_fixed() + labs(x='PCs', y='Covariates')+theme(legend.position="right")+ theme(axis.text.x = element_text(angle = 45, hjust = .8))