nplplot.multi: Plotting linkage or association statistics for multiple...

In nplplot: Plotting Linkage and Association Results

Plotting linkage or association statistics for multiple results files

Description

Wrapper function for the 'nplplot' function. Creates mutiple plots from a list of plot files, with custom graphical parameters set by header files.

Usage

nplplot.multi(filenames, plotdata = NULL, col=2, row=2, mode="l",
                output="screen", headerfiles=NULL, lgnd="page",
                customtracks=FALSE, mega2mapfile=NULL,
                pagewidth=NULL, pageheight=NULL, topmargin=0.25,
                ...)

Arguments

filenames	Vector of strings giving file names containing tables of linkage analysis results. See nplplot for a description of the file format.
plotdata	List of dataframes by chromosome containing tables of linkage analysis results. See nplplot for a description of the format.
col	Integer indicating number of columns of plots to be drawn on a page.
row	Integer signifying number of rows of plots will be drawn on a page.
mode	'p' or 'l' to denote 'portrait' or 'landscape' mode.
output	String giving file name to save plots in. If set to 'screen', plots will be displayed and not saved. The file format is determined by the filename extension: '.pdf' for PDF, or '.ps' for postscript. If no extension is provided, or is not recognized, a PDF file will be produced with '.pdf' appended to the file name.
headerfiles	Files containing R language commands to set various plot parameters, which are passed onto the nplplot command. The recommended use is to have one headerfile per plot file. For a list of parameters, consult the nplplot documentation. If the number of headerfiles is fewer than plot files, the last header file will be reused as many times as needed. If more headerfiles are provided than necessary, the last ones will be ignored.
lgnd	TRUE, FALSE, 'page' or a list consisting of plot numbers. If a single value is given, TRUE causes legends to be drawn inside every plot, FALSE omits legends altogether, and 'page' causes a legend to be drawn inside the first plot on every page. If a list of numbers is provided, only plots corresponding to these numbers will have legends.
customtracks	TRUE or FALSE. If set to TRUE, data files are created to draw custom tracks within the UCSC genome browser in BED format, as well as a combined data file to add a genome-wide track over all chromosomes present in the data. If set to TRUE, a mega2mapfile also needs to be supplied (see below).
mega2mapfile	Mega2 annotated format map file containing physical positions for all the markers present in the nplplot input data files. Rather than a file name, the name of a data.frame containing what would have been read from the file, may be given.
pagewidth	A number denoting width of the plot page in inches. If set to NULL, a width of 7.0 is used for the plot area. Assumes that a margin of 0.5 will be available around the plot area for axis annotations.
pageheight	A number denoting height of the plot page in inches. If set to NULL, a height of 10.0 is used for the plot area. Assumes that a margin of 0.5 will be available around the plot area for axis annotations.
topmargin	A number denoting the width of the outside top margin of each plot. Since this contains marker names, it may need to be increased to accommodate long names.
...	Further graphical parameters to be passed onto the 'plot', 'lines' and 'points' commands within nplplot.

Details

This function is designed for use within the Mega2 software to generate graphical output for some of the target analysis options, namely Merlin, SimWalk2 and Allegro. It calls nplplot repeatedly to create plots corresponding to each input file. The input arguments control characteristics of all plots together, whereas the header files allow customization within each plot. Thus, it is expected that there should be as many header files as there are plot data files.

This function can also be used to create custom tracks within the UCSC genome browser, as well as a genome-wide plot. To use this feature, make sure that the names of the nplplot input data files each have a "Mega2-style" chromosome extension (01 through 09 for chromosomes 1 thorugh 9, otherwise the chromosome number, or X for the human X-chromosome, 23).

To make this function more useful to other R programs, you may directly supply a data.frame for the mapfile argument and a list of data.frames for the plotdata argument and NULL for the filename argument. (The name of each list element is the corresponding chromosome.)

Value

TRUE or FALSE depending on whether all plot commands were successful.

See Also

nplplot, nplplot.old

Examples

datadir <- paste(system.file("data", package="nplplot"),
                 .Platform$file.sep, sep="")
f1 <- paste(datadir, "lods1.txt.gz", sep="")
f2 <- paste(datadir, "lods2.txt.gz", sep="")
h1 <- system.file("extdata","lods1header.R",package="nplplot")
h2 <- system.file("extdata","lods2header.R",package="nplplot")
nplplot.multi(c(f1, f2), col=1, row=2, output="screen", 
	     headerfiles=c(h1, h2), topmargin=0.5)

nplplot documentation built on May 20, 2022, 1:07 a.m.