| |
| |
| args <- commandArgs(trailingOnly = TRUE) |
| if (!length(args)) stop('Provide the path to a released RDS') |
| if (requireNamespace('SeuratObject', quietly = TRUE)) |
| suppressPackageStartupMessages(library(SeuratObject)) |
| x <- readRDS(args[1]) |
|
|
| if (inherits(x, 'Seurat')) { |
| metadata <- x@meta.data |
| ids <- colnames(x) |
| stopifnot(identical(ids, rownames(metadata)), !anyDuplicated(ids)) |
| cat('Single-cell object:', nrow(x), 'features;', length(ids), 'cells\n') |
| fields <- intersect(c('sample_id', 'patient_id', 'sample_class', 'specimen_role', |
| 'sampled_tissue', 'celltype_article', 'celltype_singler', |
| 'celltype_sctype'), names(metadata)) |
| print(head(metadata[, fields, drop = FALSE])) |
| } else if (is.list(x) && all(c('expression', 'samples') %in% names(x))) { |
| expression <- x[['expression']] |
| metadata <- x[['samples']] |
| if (is.list(expression) && !is.data.frame(expression)) { |
| if (length(args) < 2L || !args[2] %in% names(expression)) { |
| print(names(expression)) |
| stop('Multiple matrices: provide one exact MATRIX_NAME as argument 2') |
| } |
| expression <- expression[[args[2]]] |
| } |
| if (length(args) >= 3L) { |
| if (!'platform' %in% names(metadata)) stop('Platform metadata unavailable') |
| metadata <- metadata[!is.na(metadata$platform) & metadata$platform == args[3], , drop = FALSE] |
| } |
| ids <- colnames(expression) |
| if (anyDuplicated(metadata$sample_id)) |
| stop('Sample IDs recur across platforms; provide the exact PLATFORM as argument 3') |
| idx <- match(ids, metadata$sample_id) |
| stopifnot(!anyNA(idx), !anyDuplicated(ids)) |
| metadata <- metadata[idx, , drop = FALSE] |
| stopifnot(identical(ids, as.character(metadata$sample_id))) |
| cat('Bulk matrix:', nrow(expression), 'features;', length(ids), 'expression columns\n') |
| fields <- intersect(c('sample_id', 'platform', 'patient_id', 'sample_class', |
| 'sampled_tissue', 'classification_source', 'sample_type_code', |
| 'clinical_m_stage'), names(metadata)) |
| print(head(metadata[, fields, drop = FALSE])) |
| print(x[['information']]) |
| } else stop('Unsupported RDS structure') |
|
|
| if (!'sample_class' %in% names(metadata)) stop('Specimen class is not recorded') |
| print(table(metadata$sample_class, useNA = 'ifany')) |
| if (inherits(x, 'Seurat')) { |
| if (!'specimen_role' %in% names(metadata)) |
| stop('Detailed specimen roles are unavailable; inspect samples.csv before selecting tissue groups') |
| primary_ids <- ids[which(metadata$specimen_role == 'primary_tumor')] |
| metastasis_ids <- ids[which(metadata$specimen_role == 'metastatic_tumor')] |
| } else { |
| primary_ids <- ids[which(metadata$sample_class == 'Primary')] |
| metastasis_ids <- ids[which(metadata$sample_class == 'Metastasis')] |
| } |
| cat('Tissue-group selections from recorded metadata:', length(primary_ids), 'Primary;', |
| length(metastasis_ids), 'Metastasis\n') |
| |
| |
| |
| |
| |
| |
|
|
