workflow4metabolomics/heatmap

Name: heatmap

Owner: Workflow4Metabolomics

Description: Heatmap of the data matrix

Created: 2016-07-30 17:41:29.0

Updated: 2016-12-08 13:25:22.0

Pushed: 2017-06-06 15:57:56.0

Homepage: null

Size: 622

Language: R

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README

Heatmap of the data matrix

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

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
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
Licence: CeCILL
Reference history: W4M00001a_sacurine-subset-statistics
Funding: Agence Nationale de la Recherche (MetaboHUB 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

  all.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