InferCNVpy/R切换

cells.use=colnames(sc)[which(sc$CellType %in% c("Epithelial_cells","B_cells","Oligo&Astrocytes"))]


dat=as.data.frame(GetAssayData(subset(sc, cells=cells.use)))
Idents(sc)<-"CellType"
groupinfo=data.frame(v1=colnames(dat),v2=sc@active.ident[cells.use])

geneInfor=annoGene(rownames(dat),"SYMBOL",'human')
colnames(geneInfor)
geneInfor=geneInfor[with(geneInfor, order(chr, start)),c(1,4:6)]
geneInfor=geneInfor[!duplicated(geneInfor[,1]),]
length(unique(geneInfor[,1]))
head(geneInfor)
dat=dat[rownames(dat) %in% geneInfor[,1],]
dat=dat[match(geneInfor[,1], rownames(dat) ),]
dim(dat)


groupFiles='groupFiles.txt'
head(groupinfo)
write.table(groupinfo,file = groupFiles,sep = '\t',quote = F,col.names = F,row.names = F)
expFile='expFile_t.txt'
## 注意这里的exp和R版不一样，做了转置
write.table(t(dat),file = expFile,sep = '\t',quote = F)
geneFile='geneFile.txt'
write.table(geneInfor,file = geneFile,sep = '\t',quote = F,col.names = F,row.names = F)

import scanpy as sc
import infercnvpy as cnv
import pandas as pd


adata = sc.read_text('expFile_t.txt')
anno = pd.read_table('groupFiles.txt',index_col='Id') ## 这里要对文件做相应更改，添加一个列名
adata.obs['cell_groups'] = anno['cells']


gene = pd.read_table('geneFile.txt',index_col='Gene') ## 同样做相应更改，添加列名
# "chromosome", "start", "end"
adata.var=gene