adata赋值问题

import scanpy as sc 
import numpy as np 
import pandas as pd 
import scipy 


data  =scipy.sparse.load_npz("citeseq.npz")

celltype = pd.read_csv("cellTypes.csv",index_col=0)

adata = sc.AnnData(data.toarray())

adata.obs["bb"]=celltype["x"].astype(str).values
print(adata.obs["bb"])

Series不要直接赋值，而要使用values的使用

这样使用会导致最终画图的时候出错

reproduce this error

%%R -o counts -o meta

suppressMessages(library(splatter))

params <- newSplatParams()

params <- setParam(params, "nGenes", 5000)
params <- setParam(params, "batchCells", c(500,500,500))
params <- setParam(params, "batch.facLoc", 0.5)
params <- setParam(params, "batch.facScale", 0.5)
params <- setParam(params, "group.prob", c(1/3,1/3,1/3))

sim <- splatSimulate(params, method="groups", verbose=FALSE)

counts = data.frame(counts(sim))
meta = data.frame(colData(sim))

import anndata
import scanpy as sc
import bbknn

adata = anndata.AnnData(X=counts.values.T, obs=meta)

sc.pp.normalize_per_cell(adata,counts_per_cell_after=10000)
sc.pp.log1p(adata)
sc.tl.pca(adata,svd_solver='arpack')
sc.pp.neighbors(adata, n_neighbors=9)
sc.tl.umap(adata)
sc.pl.umap(adata,color=['Batch','Group'])

adata = sc.AnnData(counts)
print(adata)
adata.obs["Batch"] = meta["Batch"]
adata.obs["Group"] = meta["Group"]
sc.pp.normalize_per_cell(adata,counts_per_cell_after=10000)
sc.pp.log1p(adata)
sc.tl.pca(adata,svd_solver='arpack')
sc.pp.neighbors(adata, n_neighbors=9)
sc.tl.umap(adata)
sc.pl.umap(adata,color=['Batch','Group'])