colByValue {karyoploteR} | R Documentation

## colByValue

### 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))

[Package karyoploteR version 1.14.1 Index]