Upset Plot bulk and snRNA - two good pigs

Setup

library(UpSetR)
library(ggplot2)
library(ComplexUpset)

## 
## Attaching package: 'ComplexUpset'

## The following object is masked from 'package:UpSetR':
## 
##     upset

library(ggplot2movies)

Read in DEGs

star_brain <- read.delim("../../../bulkRNA/results/star/DEGs/LPS_Brain_gene_DEGs_FDRq0.05.txt", 
                    header = TRUE, sep = "\t")
sn_brain <- read.delim("../../results/DEGs/individual/brain_pseudo_bulk_DEGs_LPS_vs_saline_pval_0.05.tsv",
            sep = "\t", header = TRUE)

Subset lists

up_star_brain <- subset(star_brain$gene_name, star_brain$logFC > 0)
down_star_brain <- subset(star_brain$gene_name, star_brain$logFC < 0)

up_sn_brain <- subset(sn_brain$gene, sn_brain$avg_log2FC > 0)
down_sn_brain <- subset(sn_brain$gene, sn_brain$avg_log2FC < 0)

Up set plot

list_input <- list("Bulk brain up-regulated" = up_star_brain,
                   "Bulk brain down-regulated" = down_star_brain,
                   "snRNA brain up-regulated" = up_sn_brain,
                   "snRNA brain down-regulated" = down_sn_brain)
data <- fromList(list_input)

upset_gene <- upset(data, set_sizes=FALSE,
      c('Bulk brain up-regulated','Bulk brain down-regulated','snRNA brain up-regulated', 'snRNA brain down-regulated'),
  queries=list(
    upset_query(set='Bulk brain up-regulated', fill='red'),
    upset_query(set='Bulk brain down-regulated', fill='blue'),
    upset_query(set='snRNA brain up-regulated', fill='red'),
    upset_query(set='snRNA brain down-regulated', fill='blue')
  ),
  base_annotations=list(
    'Intersection size'=(
        intersection_size(
        bar_number_threshold=1,  # show all numbers on top of bars
        width=0.5,   # reduce width of the bars
      )
      # add some space on the top of the bars
      + scale_y_continuous(expand=expansion(mult=c(0, 0.05)))
      + theme(
          # hide grid lines
          panel.grid.major=element_blank(),
          panel.grid.minor=element_blank(),
          # show axis lines
          axis.line=element_line(colour='black')
      )
    )
  ),
  stripes=upset_stripes(
    geom=geom_segment(size=12),  # make the stripes larger
    colors=c('grey95', 'white')
  ),
  # to prevent connectors from getting the colorured
  # use `fill` instead of `color`, together with `shape='circle filled'`
  matrix=intersection_matrix(
      geom=geom_point(
        shape='circle filled',
        size=3,
        stroke=0.45
      )
  ),
  sort_sets='descending',
  sort_intersections='descending'
)
upset_gene

# show the genes that shared up and shared down 
shared_up <- intersect(up_star_brain, up_sn_brain)
shared_up

##  [1] "JDP2"     "MXD1"     "PARP14"   "MX2"      "BIRC2"    "NOCT"    
##  [7] "CDC25C"   "FILIP1L"  "PLOD1"    "LITAF"    "CCNL1"    "DNAJB1"  
## [13] "B4GALT5"  "PLEK"     "SLC26A11" "HSPH1"    "HUNK"     "HS6ST2"  
## [19] "ATP1A1"   "BAG3"     "HSPA8"    "HSPB8"    "DNAJA4"   "STIP1"   
## [25] "SLC38A2"  "RGS20"    "CARS1"    "CSRP2"

shared_down <- intersect(down_star_brain, down_sn_brain)
shared_down

##  [1] "LEF1"     "ARHGAP24" "ARHGAP25" "SLCO2B1"  "GRAMD1C"  "FLI1"    
##  [7] "HDAC9"    "ITGA6"    "P3H1"     "PDE3B"    "KCNK13"   "DOCK8"   
## [13] "GPC5"     "PDZRN4"   "RCSD1"    "CGNL1"    "P2RY12"   "TMCC3"   
## [19] "LRMDA"    "RASSF3"   "ST6GAL1"  "DISC1"    "PHACTR2"  "TST"     
## [25] "SOX13"    "MAN1A1"   "SLC6A20"  "ZIC2"     "BLNK"     "LOXL3"   
## [31] "TMOD3"    "SERINC5"  "NID2"     "ARHGAP15" "DOCK2"    "CDK6"    
## [37] "FAM160A1" "ZFPM2"    "IQGAP2"   "BIN2"     "TMEFF2"   "VANGL1"  
## [43] "CECR2"    "ADAMTS10" "ACOX2"    "FIGN"     "ERCC6L2"  "APBB1IP" 
## [49] "BCKDHB"   "BTBD7"    "FLT1"     "ALPL"