Heatmap (analysis)

Analysis title

Heatmap

Provider

geneXplain GmbH

Class

HeatmapCreator

Plugin

com.genexplain.stat (geneXplain Stat)

Create heatmap for a numerical data matrix

This tool creates a heatmap for the numerical data matrix provided with the input data table.

The output folder contains a TIFF image of the heatmap as well as the ordered lists of row ids (e.g. RNA or gene ids) and column ids.

The output tables can be used to extract subsets of correlated rows or columns revealed by the hierarchical clustering and/or the heatmap presentation.

Please note that the heatmap is limited to input tables with at most 5000 input rows.

Parameters

• Input table - Path to table with input data
• Colors - Color scale to apply
• Transformation - Transformation to be applied to data values
• Scaling - Scaling data values in row or column direction or none
• Width - Image width [cm]
• Height - Image height [cm]
• Resolution - Image resolution [dpi]
• Layout heights - This should be list of 2 (when no column groups are specified) or 3 (with column groups) float values separated by comma that adjust the heights of layout parts. Please refer to the documentation of R's heatmap.2 {gplots} tool for details.
• Row dendrogram - With row dendrogram
• Col dendrogram - With column dendrogram
• First group name - Name of the first column group
• First group columns - Columns assigned to first group
• Second group name - Name of the second column group
• Second group columns - Columns assigned to second group
• Third group name - Name of the third column group
• Third group columns - Columns assigned to third group
• Fourth group name - Name of the fourth column group
• Fourth group columns - Columns assigned to fourth group
• Fifth group name - Name of the fifth column group
• Fifth group columns - Columns assigned to fifth group
• Output folder - Output folder for heatmap files