xContour: Function to visualise a numeric matrix as a contour plot

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Description

xContour is supposed to visualise a numeric matrix as a contour plot.

Usage

xContour(
data,
main = "",
xlab = "",
ylab = "",
key = "",
nlevels = 50,
colormap = c("darkblue-lightblue-lightyellow-darkorange", "bwr", "jet",
"gbr", "wyr",
"br", "yr", "rainbow", "wb"),
highlight = c("none", "min", "max"),
highlight.col = "white",
x.label.cex = 0.95,
x.label.srt = 30,
signature = FALSE,
...
)

Arguments

data	a numeric matrix for the contour plot
main	an overall title for the plot
xlab	a title for the x axis. If specified, it will override 'names(dimnames(data))[1]'
ylab	a title for the y axis. If specified, it will override 'names(dimnames(data))[2]'
key	a title for the key plot (on the right)
nlevels	the number of levels to partition the input matrix values. The same level has the same color mapped to
colormap	short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names
highlight	how to highlight the point. It can be 'none' for no highlight (by default), 'min' for highlighting the point with the minimum value of the matrix, and 'max' for highlighting the point with the maximum value of the matrix
highlight.col	the highlight colors
x.label.cex	the x-axis label size
x.label.srt	the x-axis label angle (in degree from horizontal)
signature	a logical to indicate whether the signature is assigned to the plot caption. By default, it sets FALSE
...	additional graphic parameters. For most parameters, please refer to http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/filled.contour.html

Value

invisible

Note

none

See Also

xContour

Examples

x <- y <- seq(-4*pi, 4*pi, len=10)
r <- sqrt(outer(x^2, y^2, "+"))
data <- cos(r^2)*exp(-r/(2*pi))
xContour(data)
#xContour(data, signature=TRUE)

Pi documentation built on Nov. 26, 2020, 2:01 a.m.