mapColors: Maps a numeric or character vector to a color palette and...

In PhanstielLab/plotgardener: Coordinate-Based Genomic Visualization Package for R

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
)

PhanstielLab/plotgardener documentation built on July 1, 2024, 7:06 p.m.