chmNewColorMap: Create a new Color Map for use in constructing a NGCHM

In MD-Anderson-Bioinformatics/NGCHM-R: Next Generation Clustered Heat Maps

Create a new Color Map for use in constructing a NGCHM

Description

This function creates a new Color Map suitable for use in constructing Data Layers and Covariates in Next Generation Clustered Heat Maps. Color maps can be used in both discrete and continuous contents. In a discrete context, values specifies the properties of series. In a continuous context, values specifies the break points.

Usage

chmNewColorMap(
  values,
  colors = NULL,
  names = NULL,
  shapes = NULL,
  zs = NULL,
  type = "linear",
  missing.color = NULL,
  palette = NULL
)

Arguments

values	A vector specifying the series / break points for which the following colors are defined, or a data matrix.
colors	Either a string vector specifying the color to use for each series / break point, or a single integer.
names	A string vector specifying 'human-readable' names for each series / break point.
shapes	A string vector specifying the shape to use for each series.
zs	A numeric vector specifying the z order to use for each series.
type	The string "linear" (default) or "quantile" (or unique abbreviation thereof).
missing.color	A string specifying the color to use for missing data.
palette	A function(n) that returns a vector of n colors.

Details

If values is a matrix, the function will estimate a suitable sequence of color break points. For a quantile color map, the matrix data is ignored. For a linear color map, it will use equispaced values between a low value and a high value. The low value is the median of the minima of each row in the matrix, and the high value is the median of the row maxima. If the low and high values have different signs, the values will be symmetric about zero.

Value

An object of class ngchmColormap

See Also

ngchmColormap

chmNewDataLayer()

chmNewCovariateBar()

Examples

noise.colors <- chmNewColorMap(c(0, 1, 2),
  c("green", "black", "red"),
  missing.color = "yellow"
)
bar.colors <- chmNewColorMap(c("small", "big"),
  c("#00FFFF", "#FF00FF"),
  type = "quantile"
)

MD-Anderson-Bioinformatics/NGCHM-R documentation built on April 1, 2024, 12:34 p.m.