Mercurial > repos > vandelj > giant_hierarchical_clustering
comparison galaxy/wrappers/ExprHeatmapClustering.xml @ 3:dd0f4da5f68f draft
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author | vandelj |
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date | Tue, 15 Sep 2020 15:54:23 +0000 |
parents | 0b09345fa632 |
children | d75a74a93587 |
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2:ccca6ad98f78 | 3:dd0f4da5f68f |
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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 |