单细胞数据分析3（单细胞数据自动注释）

library(celldex)
#使用celldex包里的注释数据
#下载到本地
library(SingleR)
ls("package:celldex")
f = "../supp/single_ref/ref_BlueprintEncode.RData"
if(!file.exists(f)){
  ref <- celldex::BlueprintEncodeData()
  save(ref,file = f)
}
ref <- get(load(f))
#把里面的数据提取出来生成新的数据；
library(BiocParallel)
scRNA = pbmc
pred.scRNA <- SingleR(test = scRNA@assays$RNA@data, 
                      ref = ref,
                      labels = ref$label.main, 
                      clusters = scRNA@active.ident)
pred.scRNA$pruned.labels
#查看注释准确性 
plotScoreHeatmap(pred.scRNA, clusters=pred.scRNA@rownames, fontsize.row = 9,show_colnames = T)

new.cluster.ids <- pred.scRNA$pruned.labels
names(new.cluster.ids) <- levels(scRNA)
levels(scRNA)
scRNA <- RenameIdents(scRNA,new.cluster.ids)
levels(scRNA)
p2 <- DimPlot(scRNA, reduction = "umap",label = T,pt.size = 0.5) + NoLegend()
p1+p2