visHexComp: Function to visualise a component plane of a supra-hexagonal...

In hfang-bristol/supraHex: supraHex: a supra-hexagonal map for analysing tabular omics data

Description

visHexComp is supposed to visualise a supra-hexagonal grid in the context of viewport

Usage

visHexComp(
sMap,
comp,
margin = rep(0.6, 4),
area.size = 1,
colormap = c("bwr", "jet", "gbr", "wyr", "br", "yr", "rainbow", "wb"),
ncolors = 40,
zlim = c(0, 1),
border.color = "transparent",
newpage = TRUE
)

Arguments

sMap	an object of class "sMap"
comp	a component/column of codebook matrix from an object "sMap"
margin	margins as units of length 4 or 1
area.size	an inteter or a vector specifying the area size of each hexagon
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
ncolors	the number of colors specified
zlim	the minimum and maximum z values for which colors should be plotted, defaulting to the range of the finite values of z. Each of the given colors will be used to color an equispaced interval of this range. The midpoints of the intervals cover the range, so that values just outside the range will be plotted
border.color	the border color for each hexagon
newpage	a logical to indicate whether or not to open a new page

Value

invisible

Note

none

See Also

visColormap, visHexGrid

Examples

# 1) generate an iid normal random matrix of 100x10 
data <- matrix( rnorm(100*10,mean=0,sd=1), nrow=100, ncol=10)
colnames(data) <- paste(rep('S',10), seq(1:10), sep="")

# 2) sMap resulted from using by default setup
sMap <- sPipeline(data=data)

# 3) visualise the first component plane with a supra-hexagonal grid
visHexComp(sMap, comp=sMap$codebook[,1], colormap="jet", ncolors=100,
zlim=c(-1,1))

hfang-bristol/supraHex documentation built on May 24, 2021, 3:13 p.m.