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comparison heatmapper.xml @ 24:d7c9fd76e41e draft

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author bgruening
date Tue, 04 Feb 2014 09:12:07 -0500
parents 8c452f37c896
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23:8c452f37c896 24:d7c9fd76e41e
183 </tests> 183 </tests>
184 <help> 184 <help>
185 185
186 **What it does** 186 **What it does**
187 187
188 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. 188 The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
189 Those values can be visualized individually along each of the regions provided by the user in INTERVAL or BED format. 189 Like profiler, it requires that computeMatrix was run first to calculate the values.
190 In addition to the heatmap, an average profile plot is plotted on top of the heatmap (can be turned off by the user; 190
191 it can also be generated separately by the tool profiler). 191 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
192 We implemented vast optional parameters and we encourage you to play around with the min/max values displayed in the heatmap as well as 192 with the different coloring options. The most powerful option is the k-means clustering where you simply need to indicate the number of
193 with the different coloring options. If you would like to plot heatmaps for different groups of genomic regions individually, 193 groups with similar read distributions that you expect and the algorithm will do the sorting for you.
194 e.g. one plot per chromosome, simply supply each group as an individual BED file. 194
195 Do check the examples on our help page with step-by-step protocols: https://github.com/fidelram/deepTools/wiki/Example-workflows
195 196
196 197
197 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png 198 .. image:: $PATH_TO_IMAGES/visual_hm_DmelPolII.png
198 :alt: Heatmap of RNA Polymerase II ChIP-seq 199 :alt: Heatmap of RNA Polymerase II ChIP-seq
199 200
200 201
201 You can find more details in the `heatmapper wiki`_. 202 You can find more details on the tool itself on the heatmapper wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
202
203 .. _heatmapper wiki: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-heatmapper
204 203
205 204
206 ----- 205 -----
207 206
208 @REFERENCES@ 207 @REFERENCES@