visCompReorder: Function to visualise multiple component planes reorded...
In supraHex: supraHex: a supra-hexagonal map for analysing tabular omics data

Description Usage Arguments Value Note See Also Examples

visCompReorder is supposed to visualise multiple component planes reorded within a sheet-shape rectangle grid

visCompReorder(
sMap,
sReorder,
margin = rep(0.1, 4),
height = 7,
title.rotate = 0,
title.xy = c(0.45, 1),
colormap = c("bwr", "jet", "gbr", "wyr", "br", "yr", "rainbow", "wb"),
ncolors = 40,
zlim = NULL,
border.color = "transparent",
gp = grid::gpar(),
newpage = TRUE
)

`sMap`	an object of class "sMap"
`sReorder`	an object of class "sReorder"
`margin`	margins as units of length 4 or 1
`height`	a numeric value specifying the height of device
`title.rotate`	the rotation of the title
`title.xy`	the coordinates of the title
`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
`gp`	an object of class "gpar". It is the output from a call to the function "gpar" (i.e., a list of graphical parameter settings)
`newpage`	logical to indicate whether to open a new page. By default, it sets to true for opening a new page

invisible

none

visVp, visHexComp, visColorbar, sCompReorder

# 1) generate data with an iid matrix of 1000 x 9
data <- cbind(matrix(rnorm(1000*3,mean=0,sd=1), nrow=1000, ncol=3),
matrix(rnorm(1000*3,mean=0.5,sd=1), nrow=1000, ncol=3),
matrix(rnorm(1000*3,mean=-0.5,sd=1), nrow=1000, ncol=3))
colnames(data) <- c("S1","S1","S1","S2","S2","S2","S3","S3","S3")

# 2) sMap resulted from using by default setup
sMap <- sPipeline(data=data, shape=c("suprahex","trefoil")[2])

# 3) reorder component planes
sReorder <- sCompReorder(sMap=sMap, amplifier=2, metric="none")

# 4) visualise multiple component planes reorded within a sheet-shape rectangle grid
visCompReorder(sMap=sMap, sReorder=sReorder, margin=rep(0.1,4),
height=7,
title.rotate=0, title.xy=c(0.45, 1), colormap="gbr", ncolors=10,
zlim=c(-1,1),
border.color="transparent")