Set manual comparison colors in a VISTA object — set_vista_comparison

Updates metadata(x)$comparison$colors using a user-supplied named color vector. Comparison colors are used in fold-change and comparison-level plots. The color map must include all currently active comparisons.

Usage

set_vista_comparison_colors(object, color_map)

Arguments

object: A VISTA object.
color_map: Named character vector of colors, with names equal to comparison names (for example "A_VS_B").

Value

A modified VISTA object with updated comparison colors.

Examples

v <- example_vista()
comps <- names(comparisons(v))
if (length(comps)) {
  cmap <- stats::setNames(rep('#1b9e77', length(comps)), comps)
  set_vista_comparison_colors(v, cmap)
}
#> class: VISTA 
#> dim: 123 6 
#> metadata(12): de_results de_summary ... design comparison
#> assays(2): norm_counts counts
#> rownames(123): ENSG00000000003 ENSG00000000419 ... ENSG00000006607
#>   ENSG00000006625
#> rowData names(1): baseMean
#> colnames(6): SRR1039508 SRR1039512 ... SRR1039513 SRR1039517
#> colData names(14): SampleName cell ... sizeFactor sample_names
#> -------- VISTA --------
#> group column: cond_long (control, treatment1)
#> comparisons: treatment1_VS_control
#> DE source: deseq2
#> cutoffs: |log2FC| >= 1, padj <= 0.05
#> raw counts: available via counts()
#> schema: 1.1.0