xplot: Repeat specified plot across multiple columns of a matrix

In DAAGbio: Data Sets and Functions, for Demonstrations with Expression Arrays and Gene Sequences

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 = DAAGbio::coralRG$R, images = 1:6, layout = DAAGbio::coralRG$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 = DAAGbio::coralRG$R, images=1:6, layout = DAAGbio::coralRG$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()
  }

DAAGbio documentation built on Aug. 21, 2023, 1:08 a.m.