Mercurial > repos > ethevenot > heatmap

## Heatmap of the data matrix
#### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project

Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/heatmap.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/heatmap).

### Description

**Version:** 2.2.0
**Date:** 2016-07-30
**Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
**Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
**Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354)
**Licence:** CeCILL
**Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published)
**Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant)

### Installation

* Configuration file: **heatmap_config.xml**
* Image files:
    + **static/images/heatmap_workflowPositionImage.png**
    + **static/images/heatmap_workingExampleImage.png**
* Wrapper file: **heatmap_wrapper.R**
* R packages
    + **batch** from CRAN
> install.packages("batch", dep=TRUE)

### Tests

The code in the wrapper can be tested by running the **tests/heatmap_tests.R** in R

### News

##### CHANGES IN VERSION 2.2.0

NEW FEATURES

    o Default method for the correlation coefficient is now 'pearson', instead of 'spearman' previously (the latter can still be selected in the advanced parameters)

    o The 1-abs(correlation) dissimilarity is now available (in addition to the default '1-correlation') in case the sign of correlations between samples and between variables does not matter, as well as the euclidean, maximum, manhattan, canberra, binary, and minkowski dissimilarities

    o A new red-green color scale is available

***

##### CHANGES IN VERSION 2.1.2

INTERNAL MODIFICATION

    o Creating additional files for planemo and travis validation

***

##### CHANGES IN VERSION 2.0.2

INTERNAL MODIFICATION

    o Creating tests for R code

***
author	ethevenot
date	Tue, 02 Aug 2016 06:26:41 -0400
parents
children	db1d80e89156