平均表达量

library(rtracklayer)
library(dplyr)
gtf <- rtracklayer::import("gencode.v19.annotation.gtf")
gtf<-as.data.frame(gtf)
a <- unique(gtf[,12])
b <-grep("pseudogene",a,value = TRUE)
a<-gtf %>% 
  dplyr::select(c("gene_type","gene_name")) %>% 
  distinct(gene_name,.keep_all = T) %>% 
  filter(gene_type %in% b)
write.table(a,file = "./all.txt",sep = "\t",col.names = T)

DefaultAssay(integrated) <- "RNA"
integrated<- ScaleData(integrated, verbose = FALSE)
expr <- integrated@assays$RNA@counts
expr <- floor(expr)
expr <- as.matrix(expr)
#计算分组基因表达量
Idents(integrated) <- "cell_type"#设置分组为cell_type
AverageExp <- AverageExpression(integrated)
expr <- AverageExp$RNA#取RNA slot
rm(AverageExp)##减小内存
allpseu = read.table("./all.txt")
type
#allpseu = read.table("/data/chenjn/gtf/allpseu.txt")
a <- allpseu$x
row <- rownames(expr)
useful <- intersect(row,a)
expr <- expr[useful,]
ey <- expr[which(rowSums(expr)>0),]
#生成颜色；
cmcolor <- cm.colors(256)
rowcolor <- rainbow(nrow(ey), start = 0, end = 0.3)
colcolor <- rainbow(ncol(ey), start = 0, end = 0.3)
#使用默认渐变色画热图；
heatmap(ey, scale = "column",
        RowSideColors = rowcolor,
        ColSideColors = colcolor,
        margins = c(6,10),
        xlab = NULL,
        ylab = NULL)