xplot {DAAGbio} | R Documentation |
This is designed to repeat a plot, usually an image plot, across multiple columns of a matrix of gene expression values. A boxplot that shows the distribution of values appears below each panel.
xplot(data = coralRG$R, images = 1:6, layout = coralRG$printer, mfrow = c(3, 2), FUN = imgplot, device = NULL, title = NULL, width = 7.5, height = 10, paneltitles = c("1:R/G", "2:G/R", "3:R/G", "4:G/R", "5:R/G", "6:G/R"), paneltitles.line = 0.5, mar = c(3.6, 3.6, 1.6, 0.6), oma = c(0.6, 0.6, 1.6, 0.6), file = NULL)
data |
matrix of expression array values |
images |
columns of matrix for which plots are required |
layout |
layout of spots, in the order (rows of grids, columns of grids, rows of spots in a grid, columns in a grid) |
mfrow |
row by column layout of plots on a page |
FUN |
imgplot , or imageplot from limma |
device |
If NULL , plot appears on the monitor. Other
possibilities include pdf , postscript , png ,
jpeg and bitmap |
title |
A title for the page of graphs |
width |
width of plot (in) |
height |
height of plot (in) |
paneltitles |
character vector of titles for individual panels |
paneltitles.line |
height (lines) at which panel title are to appear above the upper margin of each panel |
mar |
Setting for par$mar |
oma |
Setting for par$mar |
file |
Optional file name, if output is to a file |
J. H. Maindonald
## Not run: xplot(data=coralRG$R, layout=coralRG$printer, FUN=imgplot) ## End(Not run) ## The function is currently defined as function(data = coralRG$R, images=1:6, layout = coralRG$printer, mfrow=c(3,2), FUN = imgplot, device=NULL, title=NULL, width=7.5, height=10, paneltitles=c("1:R/G","2:G/R", "3:R/G","4:G/R", "5:R/G","6:G/R"), paneltitles.line=0.5, mar=c(3.6,3.6,1.6,0.6), oma=c(0.6,0.6,1.6,0.6), file=NULL){ if(is.null(title)){title <- as.character(substitute(data)) title <- paste(title[2], title[3], sep=":") } if(is.null(file))file <- title nch <- nchar(title) if(!is.null(device)){devnam <- deparse(substitute(device)) ext <- switch(devnam, ps="ps", pdf="pdf", png="png", jpeg="jpg", bitmap="bmp") file <- paste(title,".", ext, sep="") print(file) device(file=file, width=width, height=height) } oldpar <- par(mfrow=mfrow, mgp=c(1,0.25,0), oma=oma, mar=mar) on.exit(par(oldpar)) for(i in images){ FUN(data[,i], layout=layout) mtext(side=3,line=paneltitles.line,paneltitles[i],adj=0) } mtext(side=3, line=0.25, title, outer=TRUE) if(!is.null(device))dev.off() }