Mercurial > repos > ethevenot > heatmap
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planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit bbfc13f2e4fa9e7e5b562c96d0e570318d3482d9
author | ethevenot |
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date | Tue, 06 Jun 2017 11:58:43 -0400 |
parents | db1d80e89156 |
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Heatmap of the data matrix ========================== A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/heatmap.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/heatmap). ### Description **Version:** 2.2.2 **Date:** 2016-08-04 **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 ```r install.packages("batch", dep=TRUE) ``` ### Tests The code in the wrapper can be tested by running the `runit/heatmap_runtests.R` R file ### Working example See the **W4M00001a_sacurine-subset-statistics** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published) ### News ##### CHANGES IN VERSION 2.2.2 INTERNAL MODIFICATION * Minor internal modifications ##### CHANGES IN VERSION 2.2.0 NEW FEATURES * Default method for the correlation coefficient is now 'pearson', instead of 'spearman' previously (the latter can still be selected in the advanced parameters) * 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 * A new red-green color scale is available ##### CHANGES IN VERSION 2.1.2 INTERNAL MODIFICATION * Creating additional files for planemo and travis validation ##### CHANGES IN VERSION 2.0.2 INTERNAL MODIFICATION * Creating tests for R code