R Notebook Figure 2b

1. Remove anything left in the datafiles

rm(list=ls())

If necesearry please install the following packages:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("clusterProfiler")
BiocManager::install("ReactomePA") 
BiocManager::install("rrvgo")
BiocManager::install("enrichplot")
BiocManager::install("msigdbr")
BiocManager::install("org.Hs.eg.db")
BiocManager::install("AnnotationDbi")
install.packages("ggplot2")
install.packages("glue")

Installing MULEA

Installing the BiocManager package if needed
#Installing the fgsea package with the BiocManager
BiocManager::install("fgsea")
install.packages("mulea")

2. Reading in necesearry packages

library(clusterProfiler)
library(ReactomePA)
library(rrvgo)
library(enrichplot)
library(ggplot2)
library(msigdbr)
organism ="org.Hs.eg.db"
library(organism, character.only = TRUE)
library(glue)
library(mulea)
library(tidyverse)
library(AnnotationDbi)
library(scales)

3. Data input and prepearation for enrtichment analysis THe working directory to be ecpected to be the folder of the Rmd file

PPI network propagation output

outcome_cd <- read.csv("cd_only_ppi10rnd.txt", sep="\t", row.names = 1)
head(outcome_cd)
selected_outcome_cd <- outcome_cd[outcome_cd$Z_Count>0,] 

4. Creating Figure 2/b

histogramplot_cd <- ggplot(selected_outcome_cd, aes(x=Z_Count)) + 
    geom_histogram(colour="white", fill="orange", binwidth = 50)+
    ylab("Number of individual proteins") + xlab("Number of patients") +
    geom_vline(aes(xintercept=100),
            color="black", linetype="dashed", size=1) + 
    scale_x_continuous(breaks=seq(0,1400,200)) + theme_light()
    theme(panel.background = element_rect(fill = "black")) +
    theme(plot.background = element_rect(fill = "white", colour = "white")) +
    theme(axis.title.x = element_text(colour = "black", size = 10)) +
    theme(axis.title.y = element_text(colour = "black", size = 10)) +
    theme(axis.text = element_text(color= "black", size = 10)) +
    theme(axis.line = element_line(color = "black")) +
    theme(panel.grid.minor = element_blank())
histogramplot_cd

png(file=glue("Figure_2b.png"),width=8, height=4, units="in", res=600)
histogramplot_cd
dev.off()