Fold-change heatmap — get_foldchange

Visualizes log2 fold-change matrices across comparisons with ComplexHeatmap, supporting clustering and annotations.

Usage

get_foldchange_heatmap(
  vista_obj,
  sample_comparisons,
  genes,
  repair_genes = FALSE,
  color_default = TRUE,
  col = NULL,
  show_row_names = FALSE,
  cluster_rows = TRUE,
  show_row_dend = TRUE,
  row_names_font_size = 10,
  label_specific_rows = NULL,
  label_specific_rows_gp = grid::gpar(fontsize = 5),
  show_column_names = TRUE,
  cluster_columns = TRUE,
  show_heatmap_legend = TRUE,
  kmeans_k = NULL,
  return_type = c("heatmap", "clusters", "both"),
  annotate_columns = FALSE,
  column_anno_palette = "Set2",
  heatmap_name = NULL,
  display_id = NULL,
  display_from = NULL,
  display_orgdb = NULL,
  ...
)

Arguments

vista_obj: A VISTA object with stored differential expression results.
sample_comparisons: Character vector of comparison names to include.
genes: Character vector of gene identifiers to display.
repair_genes: Logical; attempt to simplify gene_id strings by removing prefixes.
color_default: Logical; use the default diverging palette when TRUE. Set to FALSE to supply col.
col: Optional circlize::colorRamp2 color function used when color_default = FALSE.
show_row_names: Logical; draw row (gene) names.
cluster_rows: Logical; cluster rows.
show_row_dend: Logical; display the row dendrogram.
row_names_font_size: Numeric font size for row names.
label_specific_rows: Optional character vector of genes to highlight with anno_mark().
label_specific_rows_gp: grid::gpar() object controlling highlighted labels.
show_column_names: Logical; draw column labels.
cluster_columns: Logical; cluster columns.
show_heatmap_legend: Logical; display the heatmap legend.
kmeans_k: Optional integer specifying the number of k-means clusters for rows.
return_type: "heatmap", "clusters", or "both" selecting the returned value.
annotate_columns: Logical; add annotation bars keyed to the sample grouping column.
column_anno_palette: Qualitative palette name used for column annotations.
heatmap_name: Optional legend title.
display_id: Optional ID/column name to use for plot labels. If supplied
display_from: Optional source ID type for mapping (used when display_id
display_orgdb: Optional OrgDb object used for ID mapping when
...: Additional arguments forwarded to ComplexHeatmap::Heatmap().