visHexBarplot: Function to visualise codebook matrix using barplot for all...

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

Description

visHexBarplot is supposed to visualise codebook matrix using barplot for all hexagons or a specific one

Usage

visHexBarplot(
sObj,
which.hexagon = NULL,
which.hexagon.highlight = NULL,
height = 7,
margin = rep(0.1, 4),
colormap = c("customized", "bwr", "jet", "gbr", "wyr", "br", "yr",
"rainbow", "wb"),
customized.color = "red",
zeropattern.color = "gray",
gp = grid::gpar(cex = 0.7, font = 1, col = "black"),
bar.text.cex = 0.8,
bar.text.srt = 90,
newpage = TRUE
)

Arguments

sObj	an object of class "sMap" or "sTopol" or "sInit"
which.hexagon	the integer specifying which hexagon to display. If NULL, all hexagons will be visualised
which.hexagon.highlight	an integer vector specifying which hexagons are labelled. If NULL, all hexagons will be labelled
height	a numeric value specifying the height of device
margin	margins as units of length 4 or 1
colormap	short name for the predifined colormap, and "customized" for custom input (see the next 'customized.color'). The predifined colormap 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
customized.color	the customized color for pattern visualisation
zeropattern.color	the color for zero horizental line
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)
bar.text.cex	a numerical value giving the amount by which bar text should be magnified relative to the default (i.e., 1)
bar.text.srt	a numerical value giving the angle by which bar text should be orientated
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

sPipeline, visColormap

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)

# 3) plot codebook patterns using different types
# 3a) for all hexagons
visHexBarplot(sMap)
# 3b) only for the first hexagon
visHexBarplot(sMap, which.hexagon=1)

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