comparison hicPlotDistVsCounts.xml @ 4:ed96f2fd7e3f draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04

3:36360e68d5a2

            </repeat>
            <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare
them. If the `--perchr` option is given, each chromosome is plotted independently. In the case
of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple
matrices denser matrices are scaled down to match the sum of the smaller matrix.


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4:ed96f2fd7e3f

            </repeat>
            <output name="plotFile" file="hicPlotDistVsCounts_result2.png" ftype="png" compare="sim_size" delta="40000"/>
        </test>
    </tests>
    <help><![CDATA[
Relation of genomic distance and number of contacts
========================================================

| This program makes a distance vs. Hi-C counts plots. It can use several matrix files to compare
| them. If the ``--perchr`` option is given, each chromosome is plotted independently. In the case
| of more than one matrix, multiple plots are created, one per chromosome. When plotting multiple
| matrices denser matrices are scaled down to match the sum of the smaller matrix.
|
| For more information about HiCExplorer please consider our documentation on readthedocs.io_


Input
-----

Parameters
__________
- contact matrix
- skip diagonal
- per chromosome
- max depth
- plot size
- chromosome(s) to exclude

Output
-------
Output if all data in the contact matrix is considered:

.. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result1.png
   :width: 70%

Output if the distance vs. Hi-C contact counts is computed and plotted per chromosome:

.. image:: $PATH_TO_IMAGES/hicPlotDistVsCounts_result2.png
   :width: 80% 

.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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    <expand macro="citations" />
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