专栏二：单细胞空间转录组pseudobulk的使用及代码

代码一：基于count数据的加和

library(Seurat)
library(Matrix)
library(tidyverse)



#Create pseudo-bulk counts file
#obj是seurat对象
#projid是想要分组的对象 比如可以是celltype，这样得到的就是以celltype为结果的pseudobulk
pseudobulk <- function(obj){
  matrix <- GetAssayData(obj, slot="counts")
  df <- data.frame(rownames(matrix))
  samples <- as.character(unique(obj@meta.data$projid))
  for (i in samples){
    matrix <- GetAssayData(subset(obj, subset = projid == i), slot="counts")
    bulk <- data.frame(Matrix::rowSums(matrix))
    df[as.character(i)] <- bulk[1]
    
  }
  df <- data.frame(df, row.names = 1)
  names(df) <- sub("^X","",names(df)) 
  return(df)
  write.csv(df, "bulk.csv")
}

#Generate Deseq ColData
#准备下一步的分析
coldata <- function(obj){
  meta <- obj@meta.data
  meta <- meta %>% distinct(projid, .keep_all=TRUE)
  col_data <- data.frame(meta)
  col_