ggupset examples | upset plot for ggplot extention

Install

Install from GitHub: const-ae/ggupset

Quick start

The result shown above.

library(ggplot2)
library(tidyverse, warn.conflicts = FALSE)
library(ggupset)

head(tidy_movies) # test data

png('123.png',w=670,h=290)
tidy_movies %>%
  distinct(title, year, length, .keep_all=TRUE) %>%
  ggplot(aes(x=Genres)) +
    geom_bar() +
    scale_x_upset(n_intersections = 20)+
    theme_bw()
dev.off()

Expression Matrix

GeneID	Intestine BSFL10	Intestine BSFL20	Intestine BSFL30
gene-COX1	0.1461	0.0000	0.0492
gene-LOC117245643	12.3222	11.6741	10.6068
gene-LOC117245646	0.0000	0.0000	0.0292
gene-LOC117245648	0.1160	0.0439	0.0521
gene-LOC117245649	0.0000	0.0000	0.0000
gene-LOC117245651	0.8456	0.8828	0.5239

Conversion Function

Convert_up <- function(TB){
  TB_tmp = TB
  for(i in colnames(TB)){
    TB_tmp[i] = i
  }
  TB_tmp[TB == 0] = ""
  TB_t <- data.frame(t(TB_tmp), stringsAsFactors = F)
  TB_tmp$upset = as.list(TB_t)
  return(TB_tmp)
}

Expression <- read.table("../allSample.expr.csv", header = T)

TMP <- Convert_up(Expression[,-1]) # remove the GeneID
ggplot(data= TMP, aes(x=upset)) +
        geom_bar() +
        geom_text(stat='count', aes(label=after_stat(count)), vjust=-1) +
        scale_x_upset(n_intersections = 20) +
        scale_y_continuous(breaks = NULL, name = "") + expand_limits(y=c(0,20000)) +
        theme(panel.background = element_blank(), axis.line = element_line())