hmap.annotate: Add a row and column annotations to a plot-region based...

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

Add a row and column annotations to a plot-region based heatmap built with 'hmap'

Description

Annotation of rows or columns in a 'hmap'-plot. By default, rectangles aligned with either rows or columns are plotted to the right-side or lower-side of the heatmap respectively. User-specified customizations may be given to change these annotations in positioning or type.

Usage

hmap.annotate(h, rw, rw.n = length(unique(rw)), rw.col = rainbow(rw.n,
                 start = 0.05, end = 0.5), rw.wid, rw.hei, rw.pch,
                 rw.x = rep(min(h$rightlim), times =
                 length(h$rowtext$xseq)), rw.y = h$rowtext$yseq, rw.shift
                 = c(0.02, 0), cl, cl.n
                 = length(unique(cl)), cl.col = rainbow(cl.n, start =
                 0.55, end = 1), cl.wid, cl.hei, cl.pch, cl.x =
                 h$coltext$xseq, cl.y = rep(max(h$bottomlim), times =
                 length(h$coltext$yseq)), cl.shift = c(0, -0.02), ...)

Arguments

h	The list of heatmap parameters returned invisibly by the original 'hmap'-call.
rw	Annotation vector for rows 'r', each unique instance is given a different color (or pch) and plotted right-side of the corresponding heatmap rows
rw.n	Number of unique colors (or pch) to give each annotated row
rw.col	A vector for color values for unique instances in 'r' for annotating rows
rw.wid	The widths for annotation boxes for each row 'r'
rw.hei	The heights for annotation boxes for each row 'r'
rw.pch	Alternatively, instead of widths and heights user may specify a symbol 'pch' to use for annotating each row
rw.x	The x-coordinate locations for the row annotations, by default right side of heatmap itself
rw.y	The y-coordinate locations for the row annotations, by default same vertical locations as for the heatmap rows
rw.shift	Row annotation shift: a vector of 2 values, where first indicates the amount of x-axis shift desired and the second indicates the amount of y-axis shift
cl	Annotation vector for columns 'r', each unique instance is given a different color (or pch) and plotted lower-side of the corresponding heatmap columns
cl.n	Number of unique colors (or pch) to give each annotated column
cl.col	A vector for color values for unique instances in 'c' for annotating columns
cl.wid	The widths for annotation boxes for each column 'c'
cl.hei	The heights for annotation boxes for each column 'c'
cl.pch	Alternatively, instead of widths and heights user may specify a symbol 'pch' to use for annotating each column
cl.x	The x-coordinate locations for the column annotations, by default same horizontal locations as for the heatmap columns
cl.y	The y-coordinate locations for the column annotations, by default lower side of heatmap itself
cl.shift	Column annotation shift: a vector of 2 values, where first indicates the amount of x-axis shift desired and the second indicates the amount of y-axis shift
...	Additional parameters supplied either to 'rect' or 'points' function if user desired rectangles or 'pch'-based points respectively

Author(s)

Teemu Daniel Laajala <[e-mail]>

See Also

heatmap hmap.key hmap

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.