degColors {DEGreport} | R Documentation

## Make nice colors for metadata

### Description

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.

### Usage

    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)
    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)

[Package DEGreport version 1.26.0 Index]