往期推荐
GEO数据库提供的单细胞数据大致分为三类，①原始数据：fastq格式的测序数据；②经过Cellranger标准化后的10X数据；③counts数据。
VlnPlot(scobj, features = c("CD8B","CD3D"))VlnPlot(scobj, features = c("IL7R","CD3D"))VlnPlot(scobj, features = c("MS4A1", "CD79A"))VlnPlot(scobj, features = c("PPBP", "PF4"))VlnPlot(scobj, features = c("S100A9","CD14"))VlnPlot(scobj, features = c("CDKN1C"))VlnPlot(scobj, features = c("CD74"))FeaturePlot(scobj,pt.size = 0.75,reduction = "tsne",c("CD8A","IL7R","MS4A1","CD14","CDKN1C","CD1C"),order = TRUE,ncol=3)
DimPlot(scobj, reduction = "tsne", group.by ="celltype",pt.size = 1,label.size = 5,label = T,raster = F) +NoLegend() +RotatedAxis()
#subset和downsample 可以随机取每个群的细胞数DoHeatmap(subset(scobj, downsample = 500),features = marker_genes,size = 3) +theme(axis.text.y = element_text(size = 10))
参考资料
