Scanpy 计算DEG格式转换 2024-09-05

用惯了Seurat计算DEGs，使用Scanpy进行计算得到的格式会很不适应，可读性有点差，因此可以使用以下函数进行格式转换，并且根据FC进行了排序筛选Top基因。

#calculate DEG
def calculate_deg(adata,incol='leiden',use_raw=False):
    sc.tl.rank_genes_groups(adata, groupby=incol, use_raw=use_raw)
    result = adata.uns['rank_genes_groups']
    groups = result['names'].dtype.names
    df = pd.DataFrame({group + '_' + key[:1]: result[key][group] for group in groups for key in ['names', 'scores', 'logfoldchanges','pvals_adj']}).head(2000)
    splits = [ df[i] for i in df.columns]
    lnames=[]
    lscores=[]
    llog2fc=[]
    lpvalue=[]
    lcluster=[]
    for n in range(0,int(len(splits)/4)):
        lnames+=(list(splits[4*n]))
        lscores+=(list(splits[4*n+1]))
        llog2fc+=(list(splits[4*n+2]))
        lpvalue+=(list(splits[4*n+3]))
        lcluster+=(list([str(splits[4*n].name.replace('_n',''))]*len(splits[n])))

    mydict={'gene':lnames,'score':lscores,'log2fc':llog2fc,'p_value':lpvalue,'cluster':lcluster}
    out=pd.DataFrame(mydict)
    out['fc']=[ pow(2,i) for i in out['log2fc']]
    out=out.sort_values(by=['cluster','log2fc'],na_position='first',ascending=False)
    out.to_csv(incol+'_out_deg.xls',sep='\t', header=True, index=True)