Mercurial > repos > bgruening > deeptools
diff heatmapper.xml @ 24:d7c9fd76e41e draft
Uploaded
author | bgruening |
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date | Tue, 04 Feb 2014 09:12:07 -0500 |
parents | 8c452f37c896 |
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--- a/heatmapper.xml Tue Feb 04 03:38:20 2014 -0500 +++ b/heatmapper.xml Tue Feb 04 09:12:07 2014 -0500 @@ -185,22 +185,21 @@ **What it does** -The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. -Those values can be visualized individually along each of the regions provided by the user in INTERVAL or BED format. -In addition to the heatmap, an average profile plot is plotted on top of the heatmap (can be turned off by the user; -it can also be generated separately by the tool profiler). -We implemented vast optional parameters and we encourage you to play around with the min/max values displayed in the heatmap as well as -with the different coloring options. If you would like to plot heatmaps for different groups of genomic regions individually, -e.g. one plot per chromosome, simply supply each group as an individual BED file. +The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. +Like profiler, it requires that computeMatrix was run first to calculate the values. + +We implemented vast optional parameters to optimize the visual output and we encourage you to play around with the min/max values displayed in the heatmap as well as +with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of +groups with similar read distributions that you expect and the algorithm will do the sorting for you. + +Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png :alt: Heatmap of RNA Polymerase II ChIP-seq -You can find more details in the `heatmapper wiki`_. - -.. _heatmapper wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper +You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper -----