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planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit bbfc13f2e4fa9e7e5b562c96d0e570318d3482d9
author ethevenot
date Tue, 06 Jun 2017 11:58:43 -0400
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1 Heatmap of the data matrix
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2 ==========================
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
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6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/heatmap.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/heatmap).
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8 ### Description
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10 **Version:** 2.2.2
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11 **Date:** 2016-08-04
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12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
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13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
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14 **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)
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15 **Licence:** CeCILL
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16 **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published)
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17 **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)
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19 ### Installation
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21 * Configuration file: `heatmap_config.xml`
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22 * Image files:
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23 + `static/images/heatmap_workflowPositionImage.png`
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24 + `static/images/heatmap_workingExampleImage.png`
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25 * Wrapper file: `heatmap_wrapper.R`
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26 * R packages
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27 + **batch** from CRAN
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29 ```r
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30 install.packages("batch", dep=TRUE)
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31 ```
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33 ### Tests
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35 The code in the wrapper can be tested by running the `runit/heatmap_runtests.R` R file
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37 ### Working example
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39 See the **W4M00001a_sacurine-subset-statistics** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
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41 ### News
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43 ##### CHANGES IN VERSION 2.2.2
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45 INTERNAL MODIFICATION
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47 * Minor internal modifications
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49 ##### CHANGES IN VERSION 2.2.0
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51 NEW FEATURES
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53 * Default method for the correlation coefficient is now 'pearson', instead of 'spearman' previously (the latter can still be selected in the advanced parameters)
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55 * 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
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57 * A new red-green color scale is available
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59 ##### CHANGES IN VERSION 2.1.2
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61 INTERNAL MODIFICATION
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63 * Creating additional files for planemo and travis validation
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65 ##### CHANGES IN VERSION 2.0.2
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67 INTERNAL MODIFICATION
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69 * Creating tests for R code