Fold-change plotting helpers (overview) — get_foldchange

One-stop doc for fold-change plots:

get_foldchange_barplot(): log2FC by comparison (bars).
get_foldchange_boxplot(): log2FC distributions per comparison (boxes).
get_foldchange_lollipop(): log2FC stems/dots; supports 1–2 comparisons.
get_foldchange_lineplot(): log2FC trajectories across comparisons (optional clustering).

Usage

get_foldchange_lollipop(
  x,
  sample_comparison,
  genes = NULL,
  sort_by = c("input", "log2fc", "abs_log2fc"),
  palette = NULL,
  point_size = 6,
  line_size = 1.2,
  label = TRUE,
  label_digits = 2,
  display_id = NULL,
  display_from = NULL,
  display_orgdb = NULL,
  dodge_width = 0.5,
  facet_scales = "free_y",
  facet_nrow = NULL,
  facet_ncol = NULL,
  facet_by = c("auto", "gene", "comparison", "none")
)

Arguments

x: A VISTA object.
sample_comparison: Character vector of length 1 or 2 naming the comparison(s) to plot (must exist in metadata(x)$de_results).
genes: Optional character vector of gene IDs to include. When NULL, all genes in the specified comparison(s) are shown.
sort_by: How to sort genes on the y-axis: "input" (use supplied order), "log2fc" (descending log2FC; for two comparisons uses the first comparison), or "abs_log2fc" (descending max abs log2FC across comparisons).
palette: For a single comparison, named vector of colors for "pos", "neg", and "zero" sign classes (set to NULL to disable color by sign). For two comparisons, a named or unnamed vector of colors with one entry per comparison (defaults to a qualitative palette).
point_size: Numeric size of dots.
line_size: Numeric size of stems (linewidth).
label: Logical; draw numeric labels next to the dots.
label_digits: Integer; digits to show in labels when label = TRUE.
display_id: Optional column in rowData(x) used to interpret genes and to label plotted genes.
display_from: Optional source ID type for mapping when display_id is not present in rowData(x).
display_orgdb: Optional OrgDb object used for identifier mapping when display_id is not present in rowData(x).
dodge_width: Horizontal separation between comparisons when plotting two comparisons on the same axis.
facet_scales: Facet scales argument passed to facet_wrap() when facet_by != "none" (default "free_y").
facet_nrow, facet_ncol: Optional layout passed to facet_wrap() when faceting.
facet_by: Faceting mode: "auto" (default), "gene", "comparison", or "none".

Value

An object returned by this function.

A ggplot2 object.

Details

Shared arguments: x (VISTA with DE results), sample_comparisons/sample_comparison, genes, display_id for label mapping, sort_by (where supported), faceting controls (facet_*), and comparison colours pulled from Plot log2 fold changes as a lollipop chart (one or two comparisons)

Extracts log2 fold changes from stored differential expression results and plots them as stems and dots, with labels and a zero reference line. You can optionally provide two comparisons; in that case both comparisons are drawn side-by-side, coloured by comparison.

Examples

v <- example_vista()
comp <- names(comparisons(v))[1]
genes <- head(as.character(comparisons(v)[[comp]]$gene_id), 10)
p <- get_foldchange_lollipop(v, sample_comparison = comp, genes = genes)
print(p)

vista <- example_vista()
comp_name <- names(comparisons(vista))[1]
genes <- rownames(vista)[seq_len(3)]
get_foldchange_lollipop(vista, sample_comparison = comp_name, genes = genes)