library(SingleCellExperiment)
app_dir <- "/home/alex/patient_data/example"
app_dirs <- list.files('/srv/dseqr')
app_dirs <- setdiff(app_dirs,
c('indices', 'node_modules', 'pert_signature_dir',
'pert_query_dir', 'example_data.tar.gz'))
convert <- function(app_dir) {
cat('==== Working on', app_dir, '====\n')
sc_dir <- file.path(app_dir, 'single-cell')
dataset_names <- list.files(sc_dir)
dataset_dirs <- file.path(sc_dir, dataset_names)
for (i in seq_along(dataset_dirs)) {
dataset_name <- dataset_names[i]
dataset_dir <- dataset_dirs[i]
cat('working on', dataset_names[i], '...\n')
scseq_path <- file.path(dataset_dir, 'scseq.qs')
if (!file.exists(scseq_path)) next()
scseq <- qs::qread(scseq_path)
# save as seperate parts
dseqr:::split_save_scseq(scseq, dataset_dir)
# delete previous
unlink(scseq_path)
remove <- list.files(dataset_dir,
'^lm_fit|^top_tables|^cluster_stats|plots|ambient.qs|^l1000_|^cmap_|^kegg|^go',
recursive = TRUE, full.names = TRUE, include.dirs = TRUE)
unlink(remove, recursive = TRUE)
}
}
for (app_dir in app_dirs) convert(app_dir)
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