mapColors | R Documentation |
Maps a numeric or character vector to a color palette and returns the vector of colors
mapColors(vector, palette, range = NULL)
vector |
Vector to map to color. |
palette |
Color palette function. |
range |
Range of values to map for a numerical value. |
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.
Returns a character vector of color values. If the input vector is numerical, this vector will have additional 'palette' and 'range' attributes.
colorby
## 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
)
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