对细胞簇重命名

  • 1 加载R包

  • 2 读取Seurat object

  • 3 读取细胞簇的命名表

  • 4 对细胞簇重命名

1 加载R包

library(Seurat)
library(ggplot2)

2 读取Seurat object

# Remove variables
rm(list = ls())

# Set workdir
workdir <- 'F:/R_Language/R_Practice/scRNA_Seq_column'
setwd(workdir)

# Load seurat object variable
sub_cells <- readRDS(file = "data/Raw_data/sub_cells.Rds")
DT::datatable(sub_cells@meta.data)

3 读取细胞簇的命名表

dataset_loc <- 'F:/R_Language/R_Practice/scRNA_Seq_column/data/Raw_data'
label_names <- read.csv(file.path(dataset_loc, 'Rename_name.csv'), header=T)
DT::datatable(label_names)

4 对细胞簇重命名

# Rename celltype
seurat_data <- sub_cells
labers = label_names[match(as.numeric(as.character(seurat_data@active.ident)), label_names[, 1]), 2]
seurat_data$labers <- labers

# Add clusters information
metadata <- seurat_data@meta.data
metadata$new_labers <- paste0('C', metadata$cluster, ': ', metadata$labers)

# Change cluster order
a <- names(table(metadata$new_labers))
b <- gsub(":.*$", "", a)
c <- a[order(as.numeric(gsub("C", "", b)))]
metadata$new_labers2 <- factor(metadata$new_labers, levels=c)
seurat_data@meta.data <- metadata

# Visualize
DimPlot(seurat_data, reduction = "tsne", group.by = "labers", label=T, label.size=5, pt.size=1) + ggtitle('Add celltype')

DimPlot(seurat_data, reduction = "tsne", group.by = "new_labers", label=T, label.size=5, pt.size=1) + ggtitle('Add cluster inforamtion')

DimPlot(seurat_data, reduction = "tsne", group.by = "new_labers2", label=T, label.size=5, pt.size=1) + ggtitle('Change cluster order')

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