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Save VISTA tabular outputs to disk

save_vista_data.Rd

Exports selected data components from a VISTA object to CSV/TSV/RDS/XLSX.

Usage

save_vista_data(
  x,
  what = c("comparison", "comparisons", "norm_counts", "sample_info", "row_data",
    "deg_summary", "cutoffs"),
  file,
  sample_comparison = NULL,
  format = NULL,
  include_rownames = TRUE
)

Arguments

x

A VISTA object.

what

Character vector specifying which object(s) to export. Supported values are "comparison", "comparisons", "norm_counts", "sample_info", "row_data", "deg_summary", and "cutoffs".

file

Output file path.

sample_comparison

Optional comparison name used when what includes "comparison". Defaults to the first comparison in comparisons(x).

format

Output format. One of "csv", "tsv", "rds", "xlsx". If NULL, inferred from file extension.

include_rownames

Logical; include meaningful row identifiers (e.g., gene IDs or sample names) as explicit columns where applicable.

Value

Invisibly, the normalized output file path.

Examples

# \donttest{
set.seed(1)
mat <- matrix(rpois(60, lambda = 20), nrow = 10)
rownames(mat) <- paste0("gene", seq_len(nrow(mat)))
colnames(mat) <- paste0("sample", seq_len(ncol(mat)))
se <- SummarizedExperiment::SummarizedExperiment(
  assays = list(norm_counts = mat),
  colData = S4Vectors::DataFrame(
    group = rep(c("ctrl", "trt"), each = 3),
    row.names = colnames(mat)
  ),
  rowData = S4Vectors::DataFrame(
    gene_id = rownames(mat),
    row.names = rownames(mat)
  )
)
de <- data.frame(
  gene_id = rownames(mat),
  log2fc = rnorm(nrow(mat)),
  pvalue = runif(nrow(mat)),
  padj = runif(nrow(mat)),
  regulation = "Other",
  row.names = rownames(mat)
)
v <- as_vista(se, group_column = "group")
md <- S4Vectors::metadata(v)
md$de_results <- S4Vectors::SimpleList(trt_vs_ctrl = de)
md$de_summary <- S4Vectors::SimpleList(trt_vs_ctrl = as.data.frame(table(de$regulation)))
S4Vectors::metadata(v) <- md
save_vista_data(v, what = "comparison", file = tempfile(fileext = ".csv"), format = "csv")
save_vista_data(
  v,
  what = c("comparison", "norm_counts"),
  file = tempfile(fileext = ".rds"),
  format = "rds"
)
# }