Make nice colors for metadata

The function will take a metadata table and use Set2 palette when number of levels is > 3 or a set or orange/blue colors other wise.

degColors(ann, col_fun = FALSE, con_values = c("grey80", "black"),
  cat_values = c("orange", "steelblue"), palette = "Set2")

Arguments

ann	Data.frame with metadata information. Each column will be used to generate a palette suitable for the values in there.
col_fun	Whether to return a function for continuous variables (compatible with ComplexHeatmap::HeatmapAnnotation()) or the colors themself (comparible with [pheatmap::pheatmap())]). [pheatmap::pheatmap())]: R:pheatmap::pheatmap())
con_values	Color to be used for continuous variables.
cat_values	Color to be used for 2-levels categorical variables.
palette	Palette to use from brewer.pal() for multi-levels categorical variables.

Examples

data(humanGender)
library(DESeq2)
library(ComplexHeatmap)
#> Loading required package: grid
#> ========================================
#> ComplexHeatmap version 2.1.0
#> Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
#> Github page: https://github.com/jokergoo/ComplexHeatmap
#> Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
#> 
#> If you use it in published research, please cite:
#> Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
#>   genomic data. Bioinformatics 2016.
#> ========================================
idx <- c(1:10, 75:85)
dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:10, idx],
  colData(humanGender)[idx,], design=~group)
th <- HeatmapAnnotation(df = colData(dse),
                       col = degColors(colData(dse), TRUE))
Heatmap(log2(counts(dse)+0.5), top_annotation = th)

custom <- degColors(colData(dse), TRUE,
          con_values = c("white", "red"),
          cat_values = c("white", "black"),
          palette = "Set1")
th <- HeatmapAnnotation(df = colData(dse),
                        col = custom)
Heatmap(log2(counts(dse)+0.5), top_annotation = th)