# # - eval = FALSE ------------------------------------------------------------ # pkg < - c(“cellxgenedp”、“zellkonverter”,“SingleCellExperiment”、“HDF5Array”)# required_pkgs <——包裹!pkg % % rownames (installed.packages ())) # BiocManager::安装(required_pkgs ) ## ---- eval = FALSE ------------------------------------------------------------ # pkg < - c(#“mtmorgan / cellxgenedp”,“zellkonverter”、“SingleCellExperiment”,“HDF5Array " # ) ## ----------------------------------------------------------------------------- suppressPackageStartupMessages({库(zellkonverter)库(SingleCellExperiment) #加载早期避免屏蔽dplyr:: count()库(dplyr)库(cellxgenedp ) }) ## ---- eval = FALSE ------------------------------------------------------------ # cxg () ## ----------------------------------------------------------------------------- db < - db () # #----------------------------------------------------------------------------- db ## ----------------------------------------------------------------------------- 集合(db)数据集(db) (db文件 ) ## ----------------------------------------------------------------------------- collection_with_most_datasets < -数据集(db) | >计数(collection_id,sort = TRUE) | >片(1 ) ## ----------------------------------------------------------------------------- left_join (collection_with_most_datasets | >选择(collection_id),集合(db) =“collection_id”)| >一瞥 () ## ----------------------------------------------------------------------------- left_join (collection_with_most_datasets | >选择(collection_id),数据集(db),=“collection_id " ) ## ----------------------------------------------------------------------------- 数据集(db) | >选择((is.list )) ## ---- 方面 ------------------------------------------------------------------- “分析”方面(db)方面(db,“self_reported_ethnicity”)方面(db,”性 ") ## ---- african_american_female -------------------------------------------------- african_american_female < -数据集(db) | >过滤器(facets_filter(分析、“ontology_term_id”、“EFO: 0009922”),facets_filter (self_reported_ethnicity“标签”,“非裔美国人”),facets_filter(性别、“标签”、“女性 ") ) ## ----------------------------------------------------------------------------- african_american_female | >总结(total_cell_count = (cell_count总和 )) ## ----------------------------------------------------------------------------- ## 集合left_join (african_american_female | >选择(collection_id) | >不同的(),(db)集合,=“collection_id " ) ## ----------------------------------------------------------------------------- selected_files < left_join (african_american_female | >选择(dataset_id)文件(db),=“dataset_id”)selected_files # #——eval = FALSE ------------------------------------------------------------ # selected_files | > #过滤器(文件类型= =“CXG”)| > #片(1)| > # # datasets_visualize可视化一个数据集 () ## ----------------------------------------------------------------------------- local_file < - selected_files | >过滤器(dataset_id = =“3 de0ad6d - 4378 - 4 - f62 b37b ec0b75a50d94”,文件类型= =“H5AD”)| > files_download basename (local_file (dry.run = FALSE) ) ## ----------------------------------------------------------------------------- h5ad < - readH5AD h5ad (local_file, use_hdf5 = TRUE) ## ----------------------------------------------------------------------------- h5ad | > colData (h5ad) | > as_tibble() | >计数(性别、donor_id) # #——sessionInfo回声= FALSE -------------------------------------------------- sessionInfo ()