Save a VISTA plot object to disk — save_vista

Saves plot objects returned by VISTA plotting functions to file. Supports both ggplot-like objects (saved via ggplot2::ggsave()) and ComplexHeatmap objects (Heatmap / HeatmapList) saved via graphics devices.

Usage

save_vista_plot(
  plot,
  file,
  width = 8,
  height = 6,
  units = "in",
  dpi = 300,
  device = NULL,
  ...
)

Arguments

plot: A plot object. Typically ggplot, patchwork, Heatmap, or HeatmapList.
file: Output file path.
width: Plot width.
height: Plot height.
units: Units for width and height. One of "in", "cm", "mm", or "px".
dpi: Resolution for raster outputs.
device: Optional graphics device (e.g. "png", "pdf"). If NULL, inferred from file extension (defaults to "png" when missing).
...: Additional arguments passed to ggplot2::ggsave() for ggplot-like objects.

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
p <- get_pca_plot(v)
out_file <- tempfile(fileext = ".pdf")
save_vista_plot(p, file = out_file, width = 7, height = 5, units = "in")
# }