plot.gff {gff3Plotter}R Documentation

Plots Formatted Tiling Array Data on Genomic Layout

Description

Plots formatted tiling array data as well as data of further experiments on the genomic layout.

Usage

plot.gff(x, ...)

Arguments

x A list of data as obtained from a call to read.gff
... Further arguments as listed below...

Details

xrange
Genomic range to plot [necessary]
coco.tresholds
A named numeric vector of tresholds for tiling array experiments to define color coding. Names of elements define which tiling array experiments will be plotted and in which order. [necessary if tiling array experiments are to be plotted]
expro.tresholds
A named numeric vector of tresholds for further experiments to define color coding. Names of elements define which experiments will be plotted and in which order. [necessary if further experiments are to be plotted]
par.devstage
A character vector of development stages to match genomic data with. Coloring of genes will depend on the presence of the development stage information for a particular gene that matches some/any element in this argument. If omitted gene coloring will be based on the presence of anatomy information only.
par.anatomy
A character vector of anatomies to match genomic data with. Coloring of genes will depend on the presence of anatomy information for a particular gene that matches any element in this argument. UNUSED AT THE MOMENT: matches are made against muscle only.
h
A numeric vector specifiying heights of different plot elements along the vertical axis - arbitrary unit - relative values. Can be omitted, default value is automatically retrieved by a call to def.h()
nlevels
A single numeric value defining in how many layers tiling array experiments are to be displayed. Default 8.
coco.ramp
A single logical value specifying if tiling array data color coding should be made using a color ramp function. Otherwise fixed colors are used

Value

invisible(NULL)

Note

The graphical output is produced to the default device. If output to a graphic file or any other device is required, a corresponding device must be opened prior to a call to this function and closed afterwards.

Author(s)

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

See Also

read.gff, plot.gff.toFile

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]