Mercurial > repos > vandelj > giant_hierarchical_clustering

comparison galaxy/wrappers/ExprHeatmapClustering.xml @ 3:dd0f4da5f68f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author vandelj
date Tue, 15 Sep 2020 15:54:23 +0000
parents 0b09345fa632
children d75a74a93587
comparison
equal deleted inserted replaced
2:ccca6ad98f78 3:dd0f4da5f68f
1 <tool name="GIANT-Heatmap and Hierarchical clustering" id="giant_hierarchical_clustering" version="0.5.2"> 1 <tool name="GIANT-Heatmap and Hierarchical clustering" id="giant_hierarchical_clustering" version="0.5.3">
2 <description>Run hierarchical clustering and plot heatmap from expression data and/or differential expression analysis</description> 2 <description>Run hierarchical clustering and plot heatmap from expression data and/or differential expression analysis</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.8.0">r-plotly</requirement> 4 <requirement type="package" version="4.8.0">r-plotly</requirement>
5 <requirement type="package" version="1.12.0">r-dendextend</requirement> 5 <requirement type="package" version="1.12.0">r-dendextend</requirement>
6 <requirement type="package" version="0.1_20">r-ggdendro</requirement> 6 <requirement type="package" version="0.1_20">r-ggdendro</requirement>
617 <option value="no" selected="true">No</option> 617 <option value="no" selected="true">No</option>
618 <option value="log">Natural Logarithm</option> 618 <option value="log">Natural Logarithm</option>
619 <option value="log2">Base 2 Logarithm</option> 619 <option value="log2">Base 2 Logarithm</option>
620 </param> 620 </param>
621 621
622 <param name="distanceMeasure" type="select" label="Distance measure used for clustering" help="See documentation of 'Dist' R package for more information"> 622 <param name="distanceMeasure" type="select" label="Distance measure used for clustering">
623 <option value="euclidean" selected="true">euclidean</option> 623 <option value="euclidean" selected="true">euclidean</option>
624 <option value="manhattan">manhattan</option> 624 <option value="manhattan">manhattan</option>
625 <option value="binary">binary</option> 625 <option value="binary">binary</option>
626 <option value="pearson">pearson</option> 626 <option value="pearson">pearson</option>
627 <option value="spearman">spearman</option> 627 <option value="spearman">spearman</option>
628 <option value="kendall">kendall</option> 628 <option value="kendall">kendall</option>
629 <option value="absPearson">absolute pearson</option>
630 <option value="absSpearman">absolute spearman</option>
631 <option value="absKendall">absolute kendall</option>
629 </param> 632 </param>
630 633
631 <param name="aggloMethod" type="select" label="Agglomeration method used for clustering" help="See documentation of 'hclust' R method for more information"> 634 <param name="aggloMethod" type="select" label="Agglomeration method used for clustering" help="See documentation of 'hclust' R method for more information">
632 <option value="complete">complete</option> 635 <option value="complete">complete</option>
633 <option value="median">median</option> 636 <option value="median">median</option>
877 880
878 \- **Samples/comparisons clusters number** used by hierarchical clustering applied on columns/conditions. Set to 1 (ie. no clustering) if you need to conserve input columns order for visualization purposes. Columns clusters information is not included (yet) in output tabular file. 881 \- **Samples/comparisons clusters number** used by hierarchical clustering applied on columns/conditions. Set to 1 (ie. no clustering) if you need to conserve input columns order for visualization purposes. Columns clusters information is not included (yet) in output tabular file.
879 882
880 \- **Mathematical transformation** can be applied to clustered data before clustering and visualization. Data used for the filtering step are not modified by this transformation. 883 \- **Mathematical transformation** can be applied to clustered data before clustering and visualization. Data used for the filtering step are not modified by this transformation.
881 884
882 \- **Distance measure** used to cluster rows and columns. 885 \- **Distance measure** used to cluster rows and columns. For "euclidean", "manhattan" and "binary" distances the 'dist' R function is directly called, for "pearson", "spearman" and "kendall" distances the '(1-correlation)/2' term is used as a classical distance, for "absPearson", "absSpearman" and "absKendall" the 'abs(1-correlation)'' term is used.
883 886
884 \- **Agglomeration method** used to cluster rows and columns. 887 \- **Agglomeration method** used to cluster rows and columns.
885 888
886 \- **Add side bar** to vizualize factor values for displayed columns/conditions, represented as a colored side bar in the heatmap. 889 \- **Add side bar** to vizualize factor values for displayed columns/conditions, represented as a colored side bar in the heatmap.
887 890