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

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2:ccca6ad98f78

<tool name="GIANT-Heatmap and Hierarchical clustering" id="giant_hierarchical_clustering" version="0.5.2">
  <description>Run hierarchical clustering and plot heatmap from expression data and/or differential expression analysis</description>
  <requirements>
    <requirement type="package" version="4.8.0">r-plotly</requirement>
    <requirement type="package" version="1.12.0">r-dendextend</requirement>
    <requirement type="package" version="0.1_20">r-ggdendro</requirement>

      <option value="no" selected="true">No</option>
      <option value="log">Natural Logarithm</option>
      <option value="log2">Base 2 Logarithm</option>
    </param>

    <param name="distanceMeasure" type="select" label="Distance measure used for clustering" help="See documentation of 'Dist' R package for more information">
      <option value="euclidean" selected="true">euclidean</option>
      <option value="manhattan">manhattan</option>
      <option value="binary">binary</option>
      <option value="pearson">pearson</option>
      <option value="spearman">spearman</option>
      <option value="kendall">kendall</option>
    </param>

    <param name="aggloMethod" type="select" label="Agglomeration method used for clustering" help="See documentation of 'hclust' R method for more information">
      <option value="complete">complete</option>
      <option value="median">median</option>

\- **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.

\- **Mathematical transformation** can be applied to clustered data before clustering and visualization. Data used for the filtering step are not modified by this transformation.

\- **Distance measure** used to cluster rows and columns.

\- **Agglomeration method** used to cluster rows and columns.

\- **Add side bar** to vizualize factor values for displayed columns/conditions, represented as a colored side bar in the heatmap.

3:dd0f4da5f68f

<tool name="GIANT-Heatmap and Hierarchical clustering" id="giant_hierarchical_clustering" version="0.5.3">
  <description>Run hierarchical clustering and plot heatmap from expression data and/or differential expression analysis</description>
  <requirements>
    <requirement type="package" version="4.8.0">r-plotly</requirement>
    <requirement type="package" version="1.12.0">r-dendextend</requirement>
    <requirement type="package" version="0.1_20">r-ggdendro</requirement>

      <option value="no" selected="true">No</option>
      <option value="log">Natural Logarithm</option>
      <option value="log2">Base 2 Logarithm</option>
    </param>

    <param name="distanceMeasure" type="select" label="Distance measure used for clustering">
      <option value="euclidean" selected="true">euclidean</option>
      <option value="manhattan">manhattan</option>
      <option value="binary">binary</option>
      <option value="pearson">pearson</option>
      <option value="spearman">spearman</option>
      <option value="kendall">kendall</option>
      <option value="absPearson">absolute pearson</option>
      <option value="absSpearman">absolute spearman</option>
      <option value="absKendall">absolute kendall</option>
    </param>

    <param name="aggloMethod" type="select" label="Agglomeration method used for clustering" help="See documentation of 'hclust' R method for more information">
      <option value="complete">complete</option>
      <option value="median">median</option>

\- **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.

\- **Mathematical transformation** can be applied to clustered data before clustering and visualization. Data used for the filtering step are not modified by this transformation.

\- **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.

\- **Agglomeration method** used to cluster rows and columns.

\- **Add side bar** to vizualize factor values for displayed columns/conditions, represented as a colored side bar in the heatmap.