plot.gff.toFile {gff3Plotter} | R Documentation |
Redirects output of plot.gff
a PNG or a JPG file. Internally executes plot.gff
passing all ... arguments.
plot.gff.toFile(x, file, type = "jpg", width = 1024, height = 768, use.GDD = FALSE, ...)
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 |
invisible(NULL)
Oleg Sklyar, email:osklyar@ebi.ac.uk
# 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)