Export a complete VISTA asset bundle

Generates a standardized folder with selected VISTA plots, tabular outputs, and a manifest describing all saved files.

Usage

export_vista_assets(
  x,
  out_dir = "vista_assets",
  sample_comparison = NULL,
  display_id = NULL,
  include_plots = c("pca", "mds", "corr_heatmap", "deg_bar", "volcano", "ma",
    "expression_heatmap"),
  include_data = c("comparison", "norm_counts", "sample_info", "row_data", "deg_summary",
    "cutoffs"),
  plot_format = "png",
  width = 8,
  height = 6,
  heatmap_height = 10,
  units = "in",
  dpi = 300,
  top_n_labels = 50,
  heatmap_n_genes = 60,
  write_excel = FALSE,
  overwrite = TRUE
)

Arguments

x

A VISTA object.

out_dir

Output directory for exported assets.

sample_comparison

Optional comparison to use for comparison-specific outputs. Defaults to the first available comparison.

display_id

Optional gene identifier column used in labeling for volcano/MA/heatmap plots.

include_plots

Character vector of plot keys to export. Supported: "pca", "mds", "corr_heatmap", "deg_bar", "deg_pie", "deg_donut", "volcano", "ma", "expression_heatmap".

include_data

Character vector of data keys passed to save_vista_data().

plot_format

Plot format (e.g. "png" or "pdf").

width

Base plot width.

height

Base plot height.

heatmap_height

Height used specifically for expression heatmap export.

units

Plot dimension units.

dpi

Raster resolution for plots.

top_n_labels

Number of top genes to annotate in MA plots.

heatmap_n_genes

Number of top genes used in exported expression heatmaps.

write_excel

Logical; if TRUE, also writes a combined XLSX workbook for all requested include_data tables (requires writexl).

overwrite

Logical; if FALSE, aborts when out_dir already contains files.

Value

Invisibly, a list with out_dir, sample_comparison, manifest, plot_files, and data_files.

Examples

v <- example_vista()
out_dir <- file.path(tempdir(), "vista_assets_example")
res <- export_vista_assets(
  v,
  out_dir = out_dir,
  include_plots = "pca",
  include_data = "comparison"
)
names(res)
#> [1] "out_dir"           "sample_comparison" "manifest"         
#> [4] "plot_files"        "data_files"