plot.gff.toFile {gff3Plotter}R Documentation

Plots Formatted Tiling Array Data to a PNG or JPG File

Description

Redirects output of plot.gff a PNG or a JPG file. Internally executes plot.gff passing all ... arguments.

Usage

plot.gff.toFile(x, file, type = "jpg", width = 1024, height = 768, use.GDD = FALSE, ...)

Arguments

x A list of data as retrieved by a call to read.gff. Same as for plot.gff
file A single character value for an output file name with a corresponding extension
type A single character value for the type of graphic format jpg (default) or png
width A single numeric value for the image width in pixels
height A single numeric value for the image height in pixels
use.GDD A logical value specifying if GDD device (GDD R package and gd library are required) is to be used, otherwise the default or X11 (in Linux) device is used. Might be required for command line calls to this routine in versions of R prior to 2.1 where X11 could not be activated in command line mode.
... All arguments necessary for plot.gff

Value

invisible(NULL)

Author(s)

Oleg Sklyar, email:osklyar@ebi.ac.uk

See Also

read.gff, plot.gff

Examples

   # getting data file name
   dataDir = system.file("extData", package = "gff3Plotter")
   gff3File = paste(dataDir, "test.gff3", sep = "/")

   # reading the input data file
   data = read.gff(gff3File)
   xrange = c(50000, 200000)
   coco.tresholds = 0.4
   names(coco.tresholds) = "Twist"
   expro.tresholds = c(0.2, 0.5, 0.1)
   names(expro.tresholds) = c("expDmf2", "expLmd", "expTwist")
   stages = c("stage13", "stage14", "stage15", "stage16")
   anatomy = "muscle"
   #plot.gff(data, xrange, coco.tresholds, expro.tresholds, stages, anatomy)
   plot.gff.toFile(data, "test.jpg", xrange = xrange, coco.tresholds = coco.tresholds, expro.tresholds = expro.tresholds, par.devstage = stages, par.anatomy = anatomy)

[Package gff3Plotter version 1.4.0 Index]