【UCell】gene signature enrichment based on the Mann-Whitney U statistics

ucell的设计本意是通过cell type signature打分进行细胞注释，但一样可以用于其它gene set的打分

首先做好gene signature list，与seurat流程相整合。对每个细胞计算每个条目的得分，每个条目的得分会存储在seurat object- metadata里的列。

demo1: 简单快速用法

注意：ucell直接在count上走流程，可视化的时候才normalize scale等.但其他的demo都是先走标准流程。

library(remotes)
remotes::install_github("carmonalab/UCell")


library(UCell)
set.seed(123)

###加载示例数据集
library(GEOquery)
cached.object <- "demodata.rds"

if (!file.exists(cached.object)) {
  geo_acc <- "GSE115978"
  options(timeout = max(1000, getOption("timeout")))
  
  gse <- getGEO(geo_acc)
  getGEOSuppFiles(geo_acc)
  
  exp.mat <- read.csv(sprintf("%s/GSE115978_counts.csv.gz", geo_acc), header = T,
                      row.names = 1, sep = ",")
  
  saveRDS(exp.mat, cached.object)
} else {
  exp.mat <- readRDS(cached.object)
}

###define gene signatures
signatures <- list(Immune = c("PTPRC"), 
                   Macrophage = c("CTSB", "C1QB", "LAPTM5", "TYROBP", "PSAP", "C1QA", "HLA-DRA", "CTSD", "NPC2", "FCER1G"), 
                   Tcell = c("CD3D", "CD3E", "CD3G", "CD2"), 
                   Bcell = c("MS4A1", "CD79A", "CD79B", "CD19", "BANK1"),
                   Myeloid_cell = c("CD14", "LYZ", "CSF1R", "FCER1G", "SPI1", "LCK-"), 
                   Stromal = c("MMP2", "COL1A1", "COL1A2", "COL3A1", "LUM", "DCN"))

###perform ucell
u.scores <- ScoreSignatures_UCell(exp.mat, features = signatures)
u.scores[1:8, 1:2]


###show the distrobution of the scores
library(reshape2)
library(ggplot2)
melted <- reshape2::melt(u.scores)
colnames(melted) <- c("Cell", "Signature", "