2022-02-22-【迁移】CellTypist-注释免疫细胞亚群.md 2.3 KB


title: 【迁移】CellTypist 注释免疫细胞亚群 urlname: -qian-yi-CellTypist-zhu-shi-mian-yi-xi-bao-ya-qun date: 2022-02-22 13:35:24 tags: ['celltypist', '生信', '分群', '注释']

excerpt: 安装CellTypist并配置环境,加载所需的包,加载数据,将Seurat对象转换为scanpy对象,对每个细胞进行观察,对基因矩阵进行注释,组装AnnData对象,进行预测,并将预测结果添加到Seurat对象中。

安装 CellTypist

  • 配置环境

    conda create -n celltypist -c conda-forge r-base=4.1.2
    conda activate celltypist
    conda install -c conda-forge r-seurat=4.1.0 -y
    conda install -c conda-forge r-irkernel=1.3 -y
    IRkernel::installspec(name='celltypist', displayname='r-celltypist')
    conda install -c conda-forge scanpy=1.8.2 -y
    /opt/conda/envs/celltypist/bin/pip3 install celltypist -i https://pypi.tuna.tsinghua.edu.cn/simple
    conda install -c conda-forge r-reticulate=1.24 -y
    python3
    import celltypist
    celltypist.models.download_models(force_update = False)
    

    加载包

    Sys.setenv(RETICULATE_PYTHON = "/opt/conda/envs/celltypist/bin/python3.8")
    library(reticulate)
    scanpy = import("scanpy")
    celltypist = import("celltypist")
    pandas <- import("pandas")
    numpy = import("numpy")
    py_config()
    

    加载数据

    library(Seurat)
    sce <- readRDS("~/upload/yy_zhang_data/scRNA-seq/pca.celltype.rds")
    Myeloid <- subset(sce, cell_type=='Myeloid')
    

    seurat 转 scanpy

    # 数据矩阵, scanpy与Seurat的行列定义相反
    adata.X = numpy$array(t(as.matrix(Myeloid[['RNA']]@counts)))
    # 对每个细胞的观察
    adata.obs = pandas$DataFrame(Myeloid@meta.data[colnames(Myeloid[['RNA']]@counts),])
    # 对基因矩阵的注释
    adata.var = pandas$DataFrame(data.frame(gene = rownames(Myeloid[['RNA']]@counts), row.names = rownames(Myeloid[['RNA']]@counts)))
     
    # 组装AnnData对象
    adata = scanpy$AnnData(X = adata.X, obs=adata.obs, var=adata.var)
    

进行预测

model = celltypist$models$Model$load(model = 'Immune_All_AddPIP.pkl')
model$cell_types
scanpy$pp$normalize_total(adata, target_sum=1e4)
scanpy$pp$log1p(adata)
predictions = celltypist$annotate(adata, model = 'Immune_All_AddPIP.pkl', majority_voting = T)

预测添加到 seurat 对象

Myeloid = AddMetaData(Myeloid, predictions$predicted_labels)