visium_example = cellular(.silent=FALSE,
expr = "data-raw/visium/raw_feature_bc_matrix.h5",
tissue_positions = "data-raw/visium/tissue_positions_list.csv",
tech = 'visium',
method_filter = 'adaptive',
method_normalise = 'scran',
method_features = 'HVG',
dimred = c('PCA', 'UMAP', 'TSNE'),
dimred_fa = 'PCA',
collections = c('CP:REACTOME', 'CP:BIOCARTA', 'CP:PID', 'CP:KEGG', 'CP:WIKIPATHWAYS', 'h', 'GO:BP', 'GO:CC', 'GO:MF'))
usethis::use_data(visium_example, overwrite = TRUE)
jsonlite::write_json(jsonlite::fromJSON(visium_example), '../examples/visium.json')
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