Set manual group colors in a VISTA object

Updates metadata(x)$group$colors using a user-supplied named color vector. This controls group-level coloring across VISTA plots that use group mapping (for example PCA, MDS, and expression plots). The color map must include all groups currently present in the object.

Usage

set_vista_group_colors(object, color_map)

Arguments

object

A VISTA object.

color_map

Named character vector of colors, with names equal to group labels.

Value

A modified VISTA object with updated group colors.

Examples

v <- example_vista()
groups <- unique(as.character(sample_info(v)$cond_long))
gmap <- stats::setNames(c('#1b9e77', '#d95f02')[seq_along(groups)], groups)
set_vista_group_colors(v, gmap)
#> 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