QuickStart

 

Template design

  1. 1)Start Inkscape and design your own sketch. In the example below we have created a simple one showing two yeast genes known to genetically interact with each other.

  2. 2)Add a circle to the right of each gene name

  3. 3)Select a circle and open the properties dialog box. Fill the label entry with the ORF name of the gene. For example, YAL021C on the figure below.

  1. 4)Save this sketch under the name ‘My Template.svg’. Warning, you must use the ‘Inkscape SVG’ file format.

SAMPLE R CODE TO USE WITH thIS TEMPLATE

library(SVGMapping)


## Experimental Data (fake)

sampleProtLevel <- matrix(c(10, 20), nrow=2)

rownames(sampleProtLevel) <- c("YAL021C", "YFL039C")


## Gene Annotations (extracted from SGD)

data(yeastAnnotMatrix)


## Create a white-red RGB (remove Alpha) palette with 1-100 levels

myColors <- substr(heat.colors(100),1,7)


## Load template

mySVG <- loadSVG("My Template.svg")


## Map data

myDataSVG(mysvg, numData=sampleProtLevel,

           annotation=yeastAnnotMatrix,

           col=myColors)


## Show SVG

showSVG(mySVG)

In this guide we assume that Inkscape, R and SVGMapping are properly installed on your system.

Materials

In this tutorial you will need to download the following files:

  1. ๏  An SVG template without active shapes : background.svg

UNDER CONSTRUCTION