visHexBarplot: Function to visualise codebook matrix using barplot for all...
In supraHex: supraHex: a supra-hexagonal map for analysing tabular omics data

Description Usage Arguments Value Note See Also Examples

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

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
)

`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

invisible

none

sPipeline, visColormap

# 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)