R Notebook Figure 5b

Please use the same folder as work directory as the data files. 1. Remove anything left in the datafiles

If necesearry please install the following packages:2
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")
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_uc <- read.csv("uc_only_ppi_10k.txt", sep="\t", row.names = 1)
head(outcome_uc)

head(outcome_uc)

filtered_outcome_uc <- outcome_uc[outcome_uc$Z_Count>0,]
head(filtered_outcome_uc)

4. Creating Figure 5/b

histogramplot_uc <- ggplot(filtered_outcome_uc, 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())

List of 7
 $ panel.background:List of 5
  ..$ fill         : chr "black"
  ..$ colour       : NULL
  ..$ linewidth    : NULL
  ..$ linetype     : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ plot.background :List of 5
  ..$ fill         : chr "white"
  ..$ colour       : chr "white"
  ..$ linewidth    : NULL
  ..$ linetype     : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ axis.title.x    :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : chr "black"
  ..$ size         : num 10
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.title.y    :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : chr "black"
  ..$ size         : num 10
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.text       :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : chr "black"
  ..$ size         : num 10
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.line       :List of 6
  ..$ colour       : chr "black"
  ..$ linewidth    : NULL
  ..$ linetype     : NULL
  ..$ lineend      : NULL
  ..$ arrow        : logi FALSE
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_line" "element"
 $ panel.grid.minor: list()
  ..- attr(*, "class")= chr [1:2] "element_blank" "element"
 - attr(*, "class")= chr [1:2] "theme" "gg"
 - attr(*, "complete")= logi FALSE
 - attr(*, "validate")= logi TRUE

histogramplot_uc

png("Figure5b.png",width=8, height=4, units="in", res=600)
histogramplot_uc
dev.off()

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