hmap.key: Add a color key to a plot-region based heatmap built with...

In Syksy/hamlet: Hierarchical Optimal Matching and Machine Learning Toolbox

Add a color key to a plot-region based heatmap built with 'hmap'

Description

A continuous color scale key for a heatmap. By default the key is constructed according to the 'h'-object which is invisibly returned by the original 'hmap'-call. Some customization may be supplied to position the legend or to customize ticks and style.

Usage

hmap.key(h, x0 = h$leftlim[1], x1 = h$leftlim[2], y0 =
                 h$toplim[1], y1 = h$toplim[2], xlim = range(h$valseq),
                 ratio = 0.5, tick = 0.1, at = seq(from =
                 min(h$valseq), to = max(h$valseq), length.out = 5),
                 bty = "c", cex = 0.5, pos = 3, offset = c(0,0))

Arguments

h	The list of heatmap parameters returned invisibly by the original 'hmap'-call.
x0	Coordinates for the color key; left border
x1	Coordinates for the color key; right border
y0	Coordinates for the color key; lower border
y1	Coordinates for the color key; upper border
xlim	Value range for the x-axis within the key itself, by default extracted from the h-object
ratio	Ratio between y-axis coordinates to separate the key box to upper color key box and lower tick and values
tick	The vertical length in value ticks
at	The values in color key at which to plot ticks and the values at ticks
bty	Type of box to plot around the color key
cex	The zooming factor for plotting the text and other objects affected by the 'cex' parameter in 'par'
pos	The text alignment and position parameter given to the 'text' function in the key
offset	Allows offsetting legend text by absolute x,y coordinates in relation to ticks

Author(s)

Teemu Daniel Laajala <[e-mail]>

See Also

heatmap hmap hmap.annotate

Examples

# Generate some data
set.seed(1)
r1 <- replicate(30, rnorm(20))
lab <- sample(letters[1:2], 20, replace=TRUE)
r1[lab==lab[1],] <- r1[lab==lab[1],] + 2
r2a <- replicate(10, rnorm(10))
r2b <- replicate(10, rnorm(10))

# Set up a new plot region, notice we have a 2-fold wider x-axis
plot.new()
plot.window(xlim=c(0,2), ylim=c(0,1))

# Plot an example plot along with the color key and annotations for our 'lab' vector
h1 <- hmap(r1, add = TRUE)
hmap.key(h1, x1=0.18)
hmap.annotate(h1, rw = lab, rw.wid=c(0.82,0.90))

# Plot the rest to show how the coordinates are adjusted to place the heatmap(s) differently
h2a <- hmap(r2a, add = TRUE, xlim=c(1.2, 1.8), leftlim=c(1.0, 1.2), 
	rightlim=c(1.8,2.0), ylim=c(0.6, 1.0), bottomlim=c(0.5,0.6), Colv=NA)
h2b <- hmap(r2b, add = TRUE, xlim=c(1.2, 1.8), leftlim=c(1.0, 1.2), 
	rightlim=c(1.8,2.0), ylim=c(0.1, 0.5), bottomlim=c(0.0,0.1), Colv=NA)

# Show the normal plot region axes 
axis(1, at=c(0.5,1.5), c("A", "B"))

Syksy/hamlet documentation built on Aug. 28, 2023, 6:52 a.m.