# #——import_libraries --------------------------------------------------------- 库(Nebulosa)图书馆(修)库(“BiocFileCache ") ## ---- download_and_untar_file -------------------------------------------------- 黄东海< - BiocFileCache(问= FALSE) data_file < - bfcrpath(黄东海、文件。路径(" https://s3 -我们-西方- 2. - amazonaws.com/10x.files/samples/cell”、“pbmc3k”,“pbmc3k_filtered_gene_bc_matrices.tar.gz”))将(data_file, exdir = tempdir解压 ()) ## ---- read_data ---------------------------------------------------------------- < - Read10X(数据的数据。dir = file.path (tempdir(),“filtered_gene_bc_matrices”、“hg19 " )) ## ---- create_seurat_object ----------------------------------------------------- pbmc < - CreateSeuratObject(数量=数据,项目=“pbmc3k min.cells = 3, min.features = 200 ) ## ---- 质量控制 ----------------------------------------------------------------------- pbmc[[”百分比。mt"]] <- PercentageFeatureSet(pbmc, pattern = "^ mt -") pbmc <-子集(pbmc，子集= nFeature_RNA < 2500 & %。太< 5)# #——规范消息= FALSE,警告= FALSE --------------------------------------- pbmc < - SCTransform (pbmc, verbose = FALSE) # #——dim_red消息= FALSE,警告= FALSE ------------------------------------ pbmc < - RunPCA (pbmc) pbmc < - RunUMAP (pbmc,弄暗= 1:30)# #——聚类,消息= FALSE,警告= FALSE --------------------------------- pbmc < - FindNeighbors (pbmc,dim = 1:30) pbmc < - FindClusters (pbmc) # #——plot_cd4 ----------------------------------------------------------------- CD4 plot_density (pbmc。 ") ## ---- cd4_comparison ----------------------------------------------------------- FeaturePlot (pbmc, CD4) FeaturePlot (pbmc, CD4,订单= TRUE) # #——cd4_and_clustering ------------------------------------------------------- DimPlot (pbmc,标签= TRUE,击退= TRUE) # #——plot_cd3d ---------------------------------------------------------------- CD3D plot_density (pbmc。 ") ## ---- 无花果。身高= 10 ------------------------------------------------------------ p3 < - plot_density (pbmc, c(“CD8A”、“其”))p3 + plot_layout (ncol = 1) # #——无花果。身高= 14 ------------------------------------------------------------ p4 < - plot_density (pbmc, c(“CD8A”、“其”),联合= TRUE) p4 + plot_layout (ncol = 1 ) ## ----------------------------------------------------------------------------- p_list < - plot_density (pbmc, c(“CD8A”、“其”),联合= TRUE,组合= FALSE) p_list [[(p_list长度 )]] ## ---- 无花果。身高= 14 ------------------------------------------------------------ p4 < - plot_density (pbmc, c(“CD4”、“其”),联合= TRUE) p4 + plot_layout (ncol = 1) # #——无花果。身高= 10 ------------------------------------------------------------ p4 [[3]] / DimPlot (pbmc,标签= TRUE,击退= TRUE)