cd39+PD1+ t cell plot

library(tidyverse)

## ── Attaching packages ────────────────────────────────── tidyverse 1.3.0 ──

## ✔ ggplot2 3.3.0     ✔ purrr   0.3.3
## ✔ tibble  2.1.3     ✔ dplyr   0.8.5
## ✔ tidyr   1.0.2     ✔ stringr 1.4.0
## ✔ readr   1.3.1     ✔ forcats 0.4.0

## ── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()

genesets <- readRDS("input/genesets/kegg_go_btm_reactome_foointerferon.rds")

#FIG_OUT_PATH <- "plots/CITE5p/all_batches/tcr/exhaustion/2020_09_01_wherry_exhaustion_enrichment.pdf"

wherry_exhaust_up <- genesets$wherry_2007_exhaustion_up
wherry_exhaust_dn <- genesets$wherry_2007_exhaustion_dn

genesets_sub <- genesets[setdiff(names(genesets), c("wherry_2007_exhaustion_dn", "wherry_2007_exhaustion_up"))]

genesets <- genesets[sapply(genesets, length) > 0]

universe <- unique(unlist(genesets))


source("util/module_fisher.R")

res_wherry_up <- genesetFET(hits = wherry_exhaust_up, background = universe, all.sets = genesets)
res_wherry_dn <- genesetFET(hits = wherry_exhaust_dn, background = universe, all.sets = genesets)


#pdf(FIG_OUT_PATH, height = 2, width = 7)
p1 <- ggplot(res_wherry_dn %>% filter(rank(p.adj) < 10 & !grepl("wherry", geneset_name)), 
             aes(y = geneset_name, x = -log10(p.adj) ))+
        geom_col() +
        ggtitle("Wherry 2007 exhaustion\nDown")
print(p1)

p1 <- ggplot(res_wherry_up %>% filter(rank(p.adj) < 10 & !grepl("wherry", geneset_name)), 
             aes(y = geneset_name, x = -log10(p.adj) ))+
        geom_col() +
        ggtitle("Wherry 2007 exhaustion\nUp")
print(p1)

#dev.off()