scanpy学习笔记-细胞类型合并

被如何把多个cluster注释合并为同一个细胞类型困扰了很久。

最开始参考【公众号：BBio】里的方法，失败了

分析流程||scanpy单细胞分析流程2-降维聚类及差异基因鉴定

#不支持多个cluster是同一种细胞类型的格式,换一种方式添加细胞类型
new_cluster_names_unique=list(set(new_cluster_names))
new_cluster_names_unique.sort(key=new_cluster_names.index)
celltype = [new_cluster_names[int(i)] for i in adata.obs.leiden.values.tolist()]
adata.obs.leiden = celltype
adata.obs.leiden = adata.obs.leiden.astype('category')
adata.obs.leiden.cat.set_categories(new_cluster_names_unique, inplace=True)

又找了其他的：

scanpy细胞图谱细胞类型合并_今晚月亮有点圆的博客-CSDN博客

尝试了一下发现不改颜色也能成功合并。

new_cluster_names = ['epithelium_1',
                     'epithelium10',
                     'odontoblast_1',
                     'epithelium_2',
                     'epithelium_3',
                     'epithelium_4',
                     'fibroblast_1',
                     'fibroblast_2',
                     'epithelium11',
                     'epithelium_5',]

adata.rename_categories('leiden', new_cluster_names)

adata.obs['leiden'] = adata.obs['leiden'].str[:-2]

sc.pl.umap(adata, color='leiden', title='D0_umap')

ok，解决