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‎README.rst‎

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HiCExplorer
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===========
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Set of programs to process, analyze and visualize Hi-C data
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-----------------------------------------------------------
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Set of programs to process, analyze and visualize Hi-C and cHi-C data
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---------------------------------------------------------------------
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Sequencing techniques that probe the 3D organization of the genome generate large amounts of data whose processing,
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analysis and visualization is challenging. Here, we present HiCExplorer, a set of tools for the analysis and

‎bin/hicPlotSVL‎

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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from hicexplorer.hicPlotSVL import main
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if __name__ == "__main__":
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main()

‎docs/content/News.rst‎

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News and Developments
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=====================
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Release 3.3
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-----------
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**8 October 2019**
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- Fixing many bugs:
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- A bug in hicDetectLoops if a sub-matrix was very small
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- A bug in hicPlotMatrix if the region defined by --region was only a chromosome and loops should be plotted too
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- A bug in hicPlotMatrix if a loop region should be plotted and chromosomeOrder argument was used too
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- A bug in hicAggregateContacts (issue #405) if chromosomes were present in the matrix but not in the bed file
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- A bug in hicAdjustMatrix concerning a bed file and consecutive regions, see issue #343
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- A bug in hicAdjustMatrix if a chromosome is present in the matrix but not in the bed file, see issue #397
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- A bug in hicCompartmentsPolarization concerning the arguments 'quantile' and 'outliers' were interpreted as strings but should be integers
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- A bug in hicAdjustMatrix concerning the 'keep' option and how matrices are reordered internally. Thanks @LeilyR
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- Added features as requested:
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- hicPCA ignores now masked bins, see issue #342
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- chicPlotViewpoint:
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- Better legend handling on x-axis
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- Peaks are now display with their fill width
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- Add option `--pValueSignificantLevels` to categorize the p-values in x levels (e.g. 0.001 0.05 0.1)
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- chicViewpoint:
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- adding sorting via viewpoints and not by samples option (--allViewpointsList)
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- Adding an option to hicNormalize to normalize via multiplication and a use defined value (see issues #385, #424)
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- Rearrange hicAdjustMatrix to have a better accessibility to its functions from outside of main
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- Improving the documentation and fixing grammar / spelling mistakes. Thanks @simonbray
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- New script: hicPlotSVL to investigate short range vs long range ratios.
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Release 3.2
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** 22 August 2019**

‎docs/content/capture-Hi-C.rst‎

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‎docs/content/list-of-tools.rst‎

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| | | one PCA bedgraph file | polarization plot | |
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+--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
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|:ref:`hicPlotAverageRegions` | visualization | one npz file | one image | Visualization of hicAverageRegions. |
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+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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|:ref`hicPlotSVL` | analysis | one / multiple Hi-C matrices | one image, p-values file, raw data file | Computes short/long range contacts; a box plot, a p-value and raw data file |
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+--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
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|:ref:`hicMergeTADbins` | preprocessing | one Hi-C matrix, one BED file | one Hi-C matrix | Uses a BED file of domains or TAD boundaries to merge the |
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| | | | | bin counts of a Hi-C matrix. |
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""""""""""""""""""""
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:ref:`hicCompartmentsPolarization`
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""""""""""""""""""""""""""""""""""
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:ref:`hicPlotSVL`
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""""""""""""""""""""""""""""""""""
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Tools for TADs processing
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^^^^^^^^^^^^^^^^^^^^^^^^^

‎docs/content/tools/hicPlotSVL.rst‎

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.. _hicPlotSVL:
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hicPlotSVL
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==========
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.. contents::
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:local:
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Description
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^^^^^^^^^^^
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hicPlotSVL computes the ratio between short range and long range contacts per chromosome independently. Per sample one box plot is created and, if more than one sample is given,
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the computed ratios are assumed to be one distribution and a Wilcoxon rank-sum test under H0 'distributions are equal' is computed. All used data is written to a third raw data file.
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The distance to distinct short and long range contacts can be set via the `--distance` parameter; for short range the sum for all contacts smaller or equal this distance are computed, for long range contacts all contacts greater this distance.
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Usage example
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^^^^^^^^^^^^^^
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.. code-block:: bash
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$ hicPlotSVL -m hmec_10kb.cool nhek_10kb.cool hmec_10kb.cool --distance 2000000 --threads 4 --plotFileName plot.png --outFileName pvalues.txt --outFileNameData rawData.txt
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This results in three files:
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The raw data containing the sums for short range, long range and ratio per sample and chromosome.
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.. code-block:: INI
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# Created with HiCExplorer's hicPlotSVL 3.3
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# Short range vs long range contacts per chromosome: raw data
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# Short range contacts: <= 2000000
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# hmec_10kb.cool nhek_10kb.cool hmec_10kb.cool
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# Chromosome Ratio Sum <= 2000000 Sum > 2000000 Ratio Sum <= 2000000 Sum > 2000000 Ratio Sum <= 2000000 Sum > 2000000
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1 3.0399769346724543 33476834 11012200 2.79740105237572 44262902 15822866 3.0399769346724543 33476834 11012200
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2 2.7532203542810625 31723954 11522490 2.5007877714355438 47468438 18981394 2.7532203542810625 31723954 11522490
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3 2.922650759458664 26251027 8981924 2.6235211241878442 39640848 15109788 2.922650759458664 26251027 8981924
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4 2.7235598858451637 22474680 8251950 2.5572455199457864 37486882 14659086 2.7235598858451637 22474680 8251950
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5 2.9585962905193712 22716268 7678056 2.752922527526723 35445722 12875670 2.9585962905193712 22716268 7678056
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6 3.168274165465025 22872690 7219290 2.8602111006131703 33990211 11883812 3.168274165465025 22872690 7219290
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7 3.1093346580597516 19603416 6304698 2.8021236966788887 29712823 10603680 3.1093346580597516 19603416 6304698
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8 3.135391026076832 18355087 5854162 2.7964394470859024 28660624 10248970 3.135391026076832 18355087 5854162
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9 4.1147978383348125 15395763 3741560 3.819940066283481 21994046 5757694 4.1147978383348125 15395763 3741560
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10 3.448063050802953 17964043 5209894 3.1116673856502253 26270171 8442474 3.448063050802953 17964043 5209894
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11 3.5924666993070407 18651850 5191934 3.1364875011923035 26240350 8366158 3.5924666993070407 18651850 5191934
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12 3.6817551043464416 18640866 5063038 3.306662109403207 26101554 7893626 3.6817551043464416 18640866 5063038
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13 3.476204237522881 11018462 3169682 3.0976674036654805 18922281 6108558 3.476204237522881 11018462 3169682
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14 3.70550850832778 11164875 3013048 3.6226817463785164 17245704 4760480 3.70550850832778 11164875 3013048
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15 4.607631079612186 11165313 2423222 4.567998349104569 15273742 3343640 4.607631079612186 11165313 2423222
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16 4.397874357146307 10745775 2443402 3.890983210350018 14666462 3769346 4.397874357146307 10745775 2443402
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17 5.809374740402161 12168235 2094586 5.3360710927739285 14154110 2652534 5.809374740402161 12168235 2094586
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18 3.7647349280938895 9339833 2480874 3.485487446356812 15019063 4309028 3.7647349280938895 9339833 2480874
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19 6.492239632778196 8466283 1304062 5.774337450385819 9368978 1622520 6.492239632778196 8466283 1304062
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20 5.542933774973686 8962935 1617002 4.977679877778358 12009479 2412666 5.542933774973686 8962935 1617002
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21 6.665622315255486 3910374 586648 6.1843701763589225 6554715 1059884 6.665622315255486 3910374 586648
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22 8.063663557923096 4992327 619114 7.433759425439728 5932928 798106 8.063663557923096 4992327 619114
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X 2.208752982178897 14424173 6530460 2.3130534357407995 27628734 11944702 2.208752982178897 14424173 6530460
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Y 4.165021803993573 36294 8714 3.8063291139240505 45105 11850 4.165021803993573 36294 8714
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MT
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The p-values between the samples:
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.. code-block:: INI
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# Created with HiCExplorer's hicPlotSVL 3.3
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# Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum
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# Short range contacts: <= 2000000
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hmec_10kb.cool nhek_10kb.cool 0.28362036331636575
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hmec_10kb.cool hmec_10kb.cool 1.0
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nhek_10kb.cool hmec_10kb.cool 0.28362036331636575
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The box plot:
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.. image:: ../../images/plot_svl.png

‎docs/images/plot_svl.png‎

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‎docs/index.rst‎

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HiCExplorer
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===========
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Set of programs to process, normalize, analyze and visualize Hi-C data
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----------------------------------------------------------------------
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Set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data
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--------------------------------------------------------------------------------
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HiCExplorer addresses the common tasks of Hi-C data analysis from processing to visualization.
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:ref:`chicAggregateStatistic` Compiling of target regions for two samples as input for differential analysis
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:ref:`chicDifferentialTest` Differential analysis of interactions of two samples
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:ref:`chicPlotViewpoint` Plotting of viewpoint with background model and highlighting of significant and differential regions
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:ref:`hicPlotSVL` Computing short vs long range contacts and plotting the results
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=================================== ==========================================================================================================================================================
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‎hicexplorer/__init__.py‎

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import logging
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# logging.basicConfig(level=logging.DEBUG)
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logging.basicConfig(level=logging.INFO)
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logging.getLogger('matplotlib').setLevel(logging.WARNING)
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logging.getLogger('cooler').setLevel(logging.WARNING)
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logging.getLogger('hicmatrix').setLevel(logging.WARNING)
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logging.getLogger('matplotlib').setLevel(logging.ERROR)
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logging.getLogger('cooler').setLevel(logging.ERROR)
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logging.getLogger('hicmatrix').setLevel(logging.ERROR)
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logging.getLogger('numexpr').setLevel(logging.ERROR)
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import warnings

‎hicexplorer/_version.py‎

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# This file is originally generated from Git information by running 'setup.py
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# version'. Distribution tarballs contain a pre-generated copy of this file.
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__version__ = '3.2'
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__version__ = '3.3'

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