msarc.plotSVG: Draw 'msarc' Diagram

In msarc: Draw Diagrams (mis)Representing the Results of Mass Spec Experiments

Description

Given an msarc object, draw the corresponding SVG-formatted diagram.

Usage

msarc.plotSVG(msarc, file = "msarc.svg")

Arguments

msarc	an msarc object to draw.
file	a filename to write the diagram to. Will overwrite existing files without warning.

Details

The main purpose of this function is simply to draw the diagram, after a presumably interesting set of GO terms has been chosen.

Because GO category names get longer as the categories get smaller, there usually isn't room to draw them in a non-overlapping way on the diagram. For sub-categories, single letters are added as category labels, and the names are printed to the R console. The user can add names of their choice, and find a way to make them fit manually.

The object is returned with colors added, in case the user wants to draw multiple diagrams with the same colors for the same categories. Draw the first object, saving it to a variable, then create the second and use msarc.copyColors to copy the color palette from the first to the second. Save the second, copy its color palette to the third, and so on. In this way, GO categories will have the same color in all the diagrams. It's a bit tedious, but there isn't an obvious other way to achieve this.

Value

Returns the msarc object, augmented with the set of colors used.

Author(s)

Gord Brown

Examples

data('sample_complete',package="msarc")
## Not run: msarc.plotSVG(sample_complete,file="thing.svg")

msarc documentation built on May 30, 2017, 12:53 a.m.