xplot {DAAGbio}R Documentation

Repeat specified plot across multiple columns of a matrix

Description

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.

Usage

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)

Arguments

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

Author(s)

J. H. Maindonald

Examples

## 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()
  }

[Package DAAGbio version 0.5-2 Index]