SVGMapping

 
 

SVGMapping aims at displaying experimental data on custom-made SVG images. Data are used to alter attributes of graphical shapes, such as the colors, opacity. After loading a template, one can iteratively map data on given shapes. Mapping requires that shapes have been assigned a 'key' identifier as an XML attribute (eg. the SVG ID or one forged using a private namespace). This 'key' can be assigned to multiple shapes depending on the related XML schema (SVG ID are uniquely assigned). 'key' are then used to identify rows within the provided 'Data' in which 'values' are extracted. Depending on the transformation, 'values' can be map to colors (in a color list or using a color gradients..), opacity level or width. Finally since SVG is a web centric format, tooltips and redirection URLs can be automatically generated to provide an interactive experience.


This package has been designed for visual biological analysis but can be used for any scientific visual analysis. For example consider the following basic user case:  i) Create an image showing a cellular mechanism with the relevant genes displayed as circles, ii)  colored them according to their expression level in a microarray experiment, and iii) Provide mouse-over tooltips will detailed gene annotations and mouse-click URLs that redirect the browser to a detailed gene description (on a reference website). This package can generate a single SVG file (with encapsulated javascript) using around ten function calls.

Description

SVGMapping is an R package that aims at displaying experimental data on custom-made SVG images. For example, it allows you to create an image showing a cellular mechanism with relevant genes displayed as circles, and colored according to their expression level in a microarray experiment.

Installation

The SVGMapping package can be installed on any R configuration (version 2.10.0 or above). The current stable release can be installed from the CRAN repository using the command:


install.packages("SVGMapping")


Instructions to install the latest development release from the R-Forge repository are available on this page.


Documentation


A comprehensive tutorial describing all package features is included in the package and available using the command:


vignette("SVGMapping-tutorial")


The latest version of the vignette is also available here

Jean-Christophe AUDE

CEA - iBiTecS

F-91191 Gif-sur-Yvette, France


mail: jean-christophe.aude AT cea.fr

phone: +33 1 6908 2924
fax: +33 1 6908 8046

French National Agency of Research

(ANR 2009-BIOE- 002 EngineeringH2Cyano)

(c) 2011 Christophe Leplat