visCompReorder: Function to visualise multiple component planes reorded...

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

Description

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

Usage

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
)

Arguments

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

Value

invisible

Note

none

See Also

visVp, visHexComp, visColorbar, sCompReorder

Examples

# 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")

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