cosmx_example = cellular(.silent=FALSE,
expr = "data-raw/cosmx/Lung5_Rep3_exprMat_file.csv.gz",
tissue_positions = "data-raw/cosmx/Lung5_Rep3_metadata_file.csv",
tech = 'cosmx',
dimred = c('PCA', 'UMAP'),
dimred_fa = 'PCA',
collections = c('CP:REACTOME', 'CP:BIOCARTA', 'CP:PID', 'CP:KEGG', 'CP:WIKIPATHWAYS', 'h', 'GO:BP', 'GO:CC', 'GO:MF'),
org = 'hs')
usethis::use_data(cosmx_example, overwrite = TRUE)
jsonlite::write_json(jsonlite::fromJSON(cosmx_example), '../examples/cosmx.json')
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