mapColors: Map colors to values
In jefferys/fusionExpressionPlot: Plot Expression Profiles for Fused Genes

Description Usage Arguments Details Value Color Brewer Palettes See Also Examples

Maps colors to a vector of numeric data based on a palette of colors and a vector of bin ends. Can use either a named palette from the RColorBrewer package or a list of explicit colors. Data is binned and labeled with the associated color as per mapLabels. This is not intended to produce a smooth gradient, but instead compresses the information in the data into a discrete set of colors.

1 2	mapColors(x, binEnds, brewerPaletteName = "RdBu", reverse = FALSE, colors = NULL)

`x`	The vector of numeric data to map to a color
`binEnds`	The sequence of cut-points defining the bins into which the data will be split. Each bin will correspond to a color in the color vector or palette and provides for mapping each value to a color. Values exactly matching bin ends will be in the lower bin. `NA`s or values outside the range will map to `NA`. Normally the first and last bin ends are the special values `Inf` and `-Inf`. Note: bin ends will be sorted from smallest to largest before mapping, so make sure labels are ordered to match.
`brewerPaletteName`	The name of the RColorBrewer palette to use for bin labels, by default `'RdBu'`. Setting labels causes this to be ignored.
`reverse`	Reverse the order of the colors. If explicitly specifying the colors though `colors`, one could instead just reverse them. However, when using `brewerPaletteName`, this is the only way to reverse the palette order. The default value is FALSE.
`colors`	A vector of colors to use as bin names. The number of colors will have to be one less than the number of bin ends. If this is specified, any `brewerPaletteName` is ignored and the RColorBrewer package is not needed

This is really just a convenience function to allow using color brewer palettes easily when binning data. Colors are no different than other labels and can be applied generically using mapLabels. Note, this requires the RColorBrewer package if using brewerPaletteName

The vector of colors the data maps to.

If no colors are specified, a vector of colors will be assigned using the brewer palette named, 'RdBu' if not specified. Each palette comes in multiple variants with a different number of colors. The number of colors will be determined automatically from the binEnds provided. Using color brewer palettes is just a convenient shortcut to specifying a list of colors and is ignored if a vector of colors is specified. If no version of the given brewer palette has the number of levels required by the bin ends, an error will occur.

For diverging values, can have 3 - 11 bins, allowed values are:

1	BrBG PiYG PRGn PuOr RdBu RdGy RdYlBu RdYlGn Spectral

For sequential values, can have 3 - 8 bins, allowed values are:

1 2	Blues BuGn BuPu GnBu Greens Greys Oranges OrRd PuBu PuBuGn PuRd Purples RdPu Reds YlGn YlGnBu YlOrBr YlOrRd

(Note: it is Greys, not Grays)

For qualitative palettes, can have 3 to (n) bins where n varies by palette:

1 2	Accent (8), Dark2 (8), Paired (12), Pastel1 (9), Pastel2 (8), Set1 (9), Set2 (8), Set3 (12)

Note: palettes are only specified in one direction, and binEnds are always sorted from lowest to highest before using, so set reverse=TRUE if you want to reverse the color order.

mapLabels

library(RColorBrewer);

### Review from RColorBrewer
# Display available palettes
display.brewer.all()

# Display colors in a palette
paletteName <- "RdBu"
levels <- 4
RColorBrewer::brewer.pal(levels, paletteName)

### Using mapColors
x <- c(-100, -1, 0, 1, 100)
ends <- c(-Inf,-10,10,Inf)

# Map data to 3 colors using the default (RdBu) palette
mapColors( x, binEnds= ends )
#=> [1] "#EF8A62" "#F7F7F7" "#F7F7F7" "#F7F7F7" "#67A9CF"

# Map data to 3 colors using the reverse of the default (RdBu) palette
mapColors( x, binEnds= ends, reverse= TRUE)
#=> [1] "#67A9CF" "#F7F7F7" "#F7F7F7" "#F7F7F7" "#EF8A62"

# Map to a specified palette name
mapColors( x, binEnds= ends, brewerPaletteName= 'Set1' )
#=> [1] "#E41A1C" "#377EB8" "#377EB8" "#377EB8" "#4DAF4A"

# Map data using an explicit color vector
colorMap <- c('red', 'violet', 'blue')
mapColors( x, binEnds= ends, colors= colorMap)
#=> [1] "red"    "violet" "violet" "violet" "blue"

mapColors( x, binEnds= ends, colors= colorMap, reverse= TRUE)
#=> [1] "blue"   "violet" "violet" "violet" "red"