Convert numeric matrix to heatmap colors

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 jamba::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

numeric 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

character 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.

See also

Other colorjam assignment: col_div_xf(), col_linear_xf(), group2colors(), rainbowJamMulti(), vals2colorLevels(), vibrant_color_by_hue()

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);