mapColors {plotgardener} | R Documentation

## Maps a numeric or character vector to a color palette and returns the vector of colors

### Description

Maps a numeric or character vector to a color palette and returns the vector of colors

### Usage

    mapColors(vector, palette, range = NULL)

### Arguments

`vector` | Vector to map to color.
`palette` | Color palette function.
`range` | Range of values to map for a numerical value.

### Details

This function allows for the manual mapping of a numerical or factor vector to a palette of colors. For a more automatic implementation of this functionality in plotgardener functions, colorby objects can be used.

### Value

Returns a character vector of color values. If the input vector is numerical, this vector will have additional 'palette' and 'range' attributes.

### See Also

colorby

### Examples

    ## Load paired ranges data in BEDPE format
    library(plotgardenerData)
    data("IMR90_DNAloops_pairs")

    ## Add a length column
    IMR90_DNAloops_pairs$length <- (IMR90_DNAloops_pairs$start2 -
            IMR90_DNAloops_pairs$start1) / 1000

    ## Map length column to a vector of colors
    colors <- mapColors(vector = IMR90_DNAloops_pairs$length,
                palette = colorRampPalette(c("dodgerblue2", "firebrick2")))

    ## Pass color vector into bbPlotPairsArches
    heights <- IMR90_DNAloops_pairs$length / max(IMR90_DNAloops_pairs$length)
    pageCreate(width = 7.5, height = 2.1, default.units = "inches",
                showGuides = FALSE, xgrid = 0, ygrid = 0)
    params <- pgParams(
        chrom = "chr21",
        chromstart = 27900000, chromend = 30700000,
        assembly = "hg19",
        width = 7
    )

    archPlot <- plotPairsArches(
        data = IMR90_DNAloops_pairs, params = params,
        fill = colors,
        linecolor = "fill",
        archHeight = heights, alpha = 1,
        x = 0.25, y = 0.25, height = 1.5,
        just = c("left", "top"),
        default.units = "inches"
    )

    annoGenomeLabel(plot = archPlot, x = 0.25, y = 1.78, scale = "Mb")
    annoHeatmapLegend(
        plot = archPlot, fontcolor = "black",
        x = 7.0, y = 0.25,
        width = 0.10, height = 1, fontsize = 10
    )
    plotText(
        label = "Kb", rot = 90, x = 6.9, y = 0.75,
        just = c("center", "center"),
        fontsize = 10
    )

[Package plotgardener version 1.0.17 Index]