matrix2heatColors: Convert numeric matrix to heatmap colors
In jmw86069/colorjam: Jam Color manipulation functions

matrix2heatColors

R Documentation

Convert numeric matrix to heatmap colors

Description

Convert numeric matrix to heatmap colors

Usage

matrix2heatColors(
  x,
  colorV = group2colors(colnames(x)),
  defaultBaseColor = "#FFFFFF",
  transformFunc = c,
  lens = 0,
  shareLimit = TRUE,
  numLimitFactor = 0.95,
  numLimit = NULL,
  baseline = 0,
  color_below_baseline = "#FFFFFF",
  divergent = FALSE,
  rampN = 15,
  trimRamp = c(0, 0),
  verbose = FALSE,
  ...
)

Arguments

`x`	numeric matrix. If there are no `colnames(x)` they will be created using `jamba::makeNames(rep("x", ncol(x)))`.
`colorV`	character vector of R colors, named by `colnames(x)`, and recycled to `ncol(x)` if needed. If `colorV` is supplied as a list, the list elements are mapped to `colnames(x)` in order.
`defaultBaseColor`	character vector of R colors used as the default base color, when `colorV` is supplied as a vector.
`transformFunc`	function applied to numeric values before the color gradient is mapped to numeric values. For example, `transformFunc=function(i)-log10(i)` would map colors to P-value using a `-log10(p)` transformation.
`lens`	numeric value passed to `warpRamp()` to adjust the distribution of colors along the numeric range.
`shareLimit`	logical indicating whether one numeric limit `numLimit` should be used to define the numeric range for color mapping.
`numLimitFactor`	when `numLimit` is NULL, this factor is applied to the maximum numeric value to determine the `numLimit`.
`numLimit`	numeric value to define the maximum numeric value above which all numeric values are mapped to the maximum color. When set to `NULL` the `numLimitFactor` is used to define the `numLimit`.
`baseline`	numeric value to define the numeric baseline, used when `divergent=FALSE`. Values are recycled to `ncol(x)` to be applied to each column individually.
`color_below_baseline`	color used when numeric value is below the `baseline`. Values are recycled to `ncol(x)` to be applied to each column individually. When `color_below_baseline` is `NULL`, the first color in the color ramp is used for all values below the baseline.
`divergent`	logical indicating whether to apply colors to the numeric range symmetric around zero.
`rampN`	integer value to define the number of color breaks for each color gradient.
`trimRamp`	numeric vector with two values, used by `jamba::getColorRamp()` to trim the intermediate color gradient before creating the final color ramp with length `rampN`. For example, by default `jamba::getColorRamp()` creates a color gradient with 15 colorr, defined by argument `gradientN=15`, so the argument `trimRamp=c(4,2)` will trim the first 4 colors and the last 2 colors from the 15-color gradient, before generating the final color gradient with length `rampN`. The `trimRamp` argument is especially useful to remove the leading white color, or to trim the first few colors to ensure the first color in the gradient is visibly different from the background color defined by `defaultBaseColor`.
`verbose`	logical indicating whether to print verbose output.
`...`	additional arguments are passed to `jamba::getColorRamp()` for additional customization. These arguments are handled across all columns, and not a column-by-column basis.

Details

This function is intended as a rapid way of applying a color gradient to columns of numeric values, where each column has its own base color. It calls jamba::getColorRamp() for each column, and when supplied with one color, it creates a color gradient from "grey95" to the output of jamba::color2gradient().

When lens is non-zero, the color gradient is warped in order to intensify the color saturation across the numeric range.

Examples

set.seed(123);
# generate a random numeric matrix
m1 <- matrix(ncol=12, rnorm(120));
m1n <- m1;
m1n[] <- format(round(abs(m1), digits=2), trim=TRUE);
jamba::imageByColors(
   matrix2heatColors(abs(m1),
      transformFunc=c,
      divergent=FALSE,
      lens=-5,
      shareNumLimit=TRUE,
      baseline=0,
      numLimit=4),
   cellnote=m1n);

jmw86069/colorjam documentation built on March 18, 2024, 3:32 a.m.