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
xrangeGenomic range to plot [necessary]
coco.tresholdsA 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.tresholdsA 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.devstageA 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.anatomyA 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.
hA 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()
nlevelsA single numeric value defining in how many layers tiling array experiments are to be displayed. Default 8.
coco.rampA 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]