plotFeatures: Basic plotting function for obtained features

In gthar/DASiR: Distributed Annotation System in R

Description

This functions creates a basic plot with the features retrieved by getDasFeature or adds them to an existing plot.

Usage

    plotFeatures(df, col=NULL, col.start="start", col.end="end", col.id ="label", col.type="type", box.height=4, box.sep=2, pos.label=c("middle", "top", "bottom", "no"), new=TRUE, legend=TRUE, ...)

Arguments

df	data.frame with the features. Columns col.start, col.end, col.id and col.type must be present.
col	Vector of colors for each box in df. If NULL, automatic rainbow coloring for different types will be used.
col.start, col.end, col.id, col.type	Names of the columns of the data.frame from which retrieve the values
box.height, box.sep	Height and separation between boxes (in percentual points respect y-axis)
pos.label	Position of the label respect the box. If pos.label=="no", labels are disabled.
new	Open a new graphical device. If new=FALSE, boxes will be added to an existing plot (so, coordinate system must be consistent).
legend	Add legend to the plot
...	Other graphical parameters passed to plot.default

Details

This function provides a quick way to view (non-overlapped) boxes in a new or an existing plot with the features retrieved.

Notice that boxes will can be plotted overlaping the current open graphical device, so the x-coordinates must match.

Value

(none)

Author(s)

Oscar Flores <[e-mail]>

See Also

getDasFeature

Examples

    # This is UCSC Genome browser
    setDasServer(server="http://genome.ucsc.edu/cgi-bin/das")

    # Note that id now changes, we can retrieve it from getDasDsn()
    source <- "sacCer3"
    range <- GRanges(c("I"), IRanges(start=1, end=2500))
    type <- c("sgdGene")

    # We want the official genes from 'sdgGene' in the range I:1-2500
    features <- getDasFeature(source, range, type)
    print(features)

    plotFeatures(features)

gthar/DASiR documentation built on May 17, 2019, 8:56 a.m.