singleR细胞注释PBMC

singleR细胞注释

##调用第三方包

library(SingleR)

library(celldex)

library(qs)

library(Seurat)

##备份

setwd("~/pbmc/04.cell_type_ann/")

pbmc=qread("pbmc.added.celltype.qs")

pbmc_singleR <- pbmc

##载入参考数据集

MID <- MonacoImmuneData()

##提取表达矩阵

pbmc_count <- GetAssayData(object = pbmc_singleR,layer = "data")

##预测

pred <- SingleR(test = pbmc_count,

ref = MID,

assay.type.test=1,

labels = MID$label.main,

clusters = pbmc_singleR$seurat_clusters)

pred

##提取并更新到pbmc_singleR中

pbmc_singleR$singleR_anno <- pred$labels[match(pbmc_singleR$seurat_clusters,rownames(pred))]

DimPlot(pbmc_singleR, reduction = "umap", label = TRUE, repel = TRUE,pt.size = 1.5,group.by = "singleR_anno")