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Fold-change heatmap

Source: R/bioccheck_roxygen_fixes.R, R/viz_related.R
get_foldchange_heatmap.Rd

Visualizes log2 fold-change matrices across comparisons with ComplexHeatmap, supporting clustering and annotations. With only a VISTA object, the function will plot the top DE genes across the stored comparisons.

Usage

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

Arguments

x

A VISTA object with stored differential expression results.

sample_comparisons

Optional character vector of comparison names to include. Defaults to all available comparisons.

genes

Optional character vector of gene identifiers to display. When omitted, VISTA selects the top DE genes from each comparison by absolute log2 fold-change.

top_n

Integer number of genes to select per comparison when genes = NULL. Defaults to 10.

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

repair_genes

Logical; attempt to simplify gene_id strings by removing prefixes.

show_row_names

Logical; draw row (gene) names. When NULL, VISTA turns labels on automatically for auto-selected genes.

label_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_rows

Logical; cluster rows.

show_row_dend

Logical; display the row dendrogram.

cluster_columns

Logical; cluster columns.

kmeans_k

Optional integer specifying the number of k-means clusters for rows.

annotate_columns

Logical; add an annotation bar identifying each column's comparison. Columns of a fold-change heatmap are comparisons, so the bar is keyed to the comparison rather than to sample metadata.

column_anno_palette

Qualitative palette name used for column annotations.

column_anno_colors

Optional named list of colour vectors overriding column_anno_palette per annotation level, matching get_expression_heatmap(). Defaults to the object's comparison colours, so the heatmap agrees with the other comparison-coloured plots.

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.

heatmap_name

Optional legend title.

show_heatmap_legend

Logical; display the heatmap legend.

return_type

One of "plot" (default), "data", or "both". The legacy values "heatmap" and "clusters" are still accepted and warn.

...

Additional arguments forwarded to ComplexHeatmap::Heatmap().

Value

A ComplexHeatmap::Heatmap object, a tibble of k-means cluster assignments, or a list of both, depending on return_type.

A ComplexHeatmap object, a cluster data frame, or a list containing both depending on return_type.

Examples

v <- example_vista()
comp <- names(comparisons(v))[1]
genes <- unique(stats::na.omit(as.character(comparisons(v)[[comp]]$gene_id)))[seq_len(20)]
if (requireNamespace('ComplexHeatmap', quietly = TRUE) &&
    requireNamespace('circlize', quietly = TRUE)) {
  hm <- get_foldchange_heatmap(
    v,
    sample_comparisons = comp,
    genes = genes,
    return_type = 'heatmap'
  )
  ComplexHeatmap::draw(hm)
}
#> Warning: `return_type = "heatmap"` in `get_foldchange_heatmap()` is deprecated. Use `return_type = "plot"` instead. It becomes defunct in VISTA 1.4.0.
#> This warning is displayed once every 8 hours.

v <- example_vista()
if (requireNamespace("ComplexHeatmap", quietly = TRUE) &&
    requireNamespace("circlize", quietly = TRUE)) {
  hm <- get_foldchange_heatmap(v, return_type = "plot")
  ComplexHeatmap::draw(hm)
}