Fold-change line plot across comparisons

Plots log2 fold-change trajectories for selected genes across multiple comparisons, optionally clustering genes.

Usage

get_foldchange_lineplot(
  x,
  sample_comparisons,
  genes = NULL,
  km = NULL,
  facet_clusters = FALSE,
  line_transparency = 0.5,
  show_average_line = TRUE,
  average_line_color = NULL,
  average_line_size = 1,
  average_line_summary_method = "median"
)

Arguments

x

A VISTA object containing differential expression results.

sample_comparisons

Character vector of comparison names to include.

genes

Optional character vector of gene identifiers to plot. Defaults to all genes.

km

Optional integer specifying the number of k-means clusters to compute; NULL disables clustering.

facet_clusters

Logical; facet the plot by cluster when k-means clustering is requested.

line_transparency

Numeric alpha applied to individual gene lines.

show_average_line

Logical; overlay a summary line per cluster when TRUE.

average_line_color

Color used for the summary line. When NULL, uses the first comparison color (if stored) for consistency across plots.

average_line_size

Numeric line width for the summary line.

average_line_summary_method

Character string selecting "median" or "mean" for the summary statistic.