colByValue: colByValue

In karyoploteR: Plot customizable linear genomes displaying arbitrary data

Description

Given a set of values, return a color for each of them based on their numeric value.

Usage

colByValue(value, colors, min=NULL, max=NULL)

Arguments

value	A vector of numeric values
colors	(color) The colors to built the color ramp. Refer to colorRamp for more details.
min	(NULL or numeric) The min value used to normalize the values. If NULL, min(value) will be used. (defaults to NULL)
max	(NULL or numeric) The max value used to normalize the values. If NULL, max(value) will be used. (defaults to NULL)

Details

A color ramp (similar to a gradient) will be built using the colors in the 'colors' parameter using colorRamp. Values will be normalized to [0,1] using 'min' and 'max' (if NULL, min(value) will be 0 and max(value) will be 1) and these values will be used to determine the color. It uses

Value

A vector of colors

Note

Alpha values (transparency) are also used in the color computation (see examples)

See Also

kpPoints, colByChr

Examples

colByValue(c(0,0.25,0.5,0.75,1), colors=c("red", "green"))
colByValue(c(0,0.25,0.5,0.75,1), colors=c("#00000000", "#00000011"))

data <- toGRanges("chr1", c(1e6*1:245), c(1e6*1:245)+10)
data$y <- rnorm(n = length(data), mean = 0.5, sd = 0.15)

kp <- plotKaryotype(chromosomes="chr1")
kpPoints(kp, data=data, r0=0, r1=0.3)
kpPoints(kp, data=data, r0=0.35, r1=0.65, col=colByValue(data$y, colors=c("black", "green")) )
kpPoints(kp, data=data, r0=0.7, r1=1, col=colByValue(data$y, colors=c("black", "green"), min=0.4, max=0.6))

kp <- plotKaryotype(chromosomes="chr1")
kpPoints(kp, data=data, r0=0, r1=0.3, col=colByValue(data$y, colors=c("#00000000", "#000000FF")))
kpPoints(kp, data=data, r0=0.35, r1=0.65, col=colByValue(data$y, colors=c("black", "orange", "green")) )
kpPoints(kp, data=data, r0=0.7, r1=1, col=colByValue(data$y, colors=c("red", "#00000022","#00000022", "green"),min=0.4, max=0.6))

karyoploteR documentation built on Nov. 8, 2020, 5:52 p.m.