fromto-bioinforbook

引入R包

library("fromto")
library(Seurat)

采用bplot_scmarkers函数分析Seurat对象scRNA，指定meta.data中的分组为Celltype (minor-lineage)

plot_bubble = bplot_scmarkers(scRNA,
                              label = "Celltype (minor-lineage)",
                              width = 25,
                              height = 8,
                              Neutrophils = NA,
                              Basophils = NA,
                              Eosinophils = NA,
                              Masts = c("TPSAB1", "TPSB2", "CPA3"),
                              DCs = c("CLEC10A", "LAMP3", "ITGAX"),
                              cDC1s = NA,
                              cDC2s = NA,
                              pDCs = c("CLEC4C"),
                              Plasmas = c("IGHG1", "MZB1"),
                              Bs = c("CD79A", "CD79B"),
                              Ts = c("CD3D", "CD3E", "CD3G"),
                              CD4s = c("CD4"),
                              CD8s = c("CD8A", "CD8B"),
                              Texs = c("LAG3", "TIGIT", "PDCD1", "HAVCR2"),
                              Tregs = c("FOXP3"),
                              Tns = c("TCF7", "SELL", "LEF1", "CCR7"),
                              Teffs = c("PRF1", "GZMB"),
                              NKs = c("KLRD1", "KLRC3", "NCAM1"),
                              Monocytes = c("CD14", "FCGR3A"),
                              Macrophages = c("LYZ", "CD68"),
                              Cardiomyocytes = NA,
                              Fibroblasts = c("DCN", "COL1A1"),
                              Endothelials = c("TEK", "PECAM1"),
                              Mesothelials = NA,
                              SMCs = NA,
                              Epithelials = c("EPCAM", "KRT19"),
                              Prolifs = c("MKI67")
                              )