Merge pull request #733 from deeptools/interintratadratio

Interintratadratio

bin/hicInterIntraTAD

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from hicexplorer.hicInterIntraTAD import main
+
+if __name__ == "__main__":
+    main()

docs/content/list-of-tools.rst

@@ -50,6 +50,8 @@ Tools for TADs processing
     tools/hicMergeDomains
     tools/hicDifferentialTAD
     tools/hicMergeTADbins
+    tools/hicInterIntraTAD
+
 
 Tools for Hi-C and TADs visualization
 -------------------------------------
@@ -113,6 +115,8 @@ For single-cell Hi-C data analysis please use `scHiCExplorer <https://schicexplo
 |:ref:`hicDifferentialTAD`             | analysis         | two Hi-C matrices                 | two diff_tad files: accepted H0 and         | Identifies differential Topologically Associating Domains (TADs) between          |
 |                                      |                  | one TAD domain file               | rejected H0. Similar to BED6                | two Hi-C matrices                                                                 |
 +--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
+|:ref:`hicInterIntraTAD`             | analysis         | Hi-C matrix, TAD boundaries       | data file and a plot                        | Computes and extracts TAD data. Creates a plot for the inter/intra contact ratio. |
++--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
 |:ref:`hicPlotMatrix`                  | visualization    | hicMatrix object                  | a heatmap of Hi-C contacts                  | Plots a Hi-C matrix as a heatmap                                                  |
 +--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
 |:ref:`hicPlotTADs`                    | visualization    | hicMatrix object, a config file   | Hi-C contacts on a given region, along with | Plots TADs as a track that can be combined with other tracks                      |

docs/content/tools/hicInterIntraTAD.rst

@@ -0,0 +1,24 @@
+.. _hicInterIntraTAD:
+
+hicInterIntraTAD
+================
+
+.. argparse::
+   :ref: hicexplorer.hicInterIntraTAD.parse_arguments
+   :prog: hicInterIntraTAD
+
+This tool computes and extracts for given TADs the inter-left, inter-right and intra-TAD data: the absolute number of contacts, the density (non-zero contacts / all possible contacts) and the ratio of inter-left/intra, inter-right/intra and (inter-left + inter-right)/intra TAD contacts.
+The data is saved in one file where it can be used for further, user-specific computations outside of HiCExplorer. Also a scatter plot of the ratio inter-left/intra vs. inter-right/intra is created.
+
+.. code-block:: INI
+
+    # Created with HiCExplorer's hicInterIntraTAD version 3.7-dev
+    # Chromosome	start	end	name	score	strand	inter_left_sum	inter_right_sum	inter_left_density	inter_right_density	inter_left_number_of_contacts	inter_right_number_of_contacts	inter_left_number_of_contacts_nnz	inter_right_number_of_contacts_nnz	intra_sum	intra_number_of_contacts	intra_number_of_contacts_nnz	intra_density	inter_left_intra_ratio	inter_right_intra_ratio	inter_left_inter_right_intra_ratio
+    chr1	4400000	6200000	ID_0.01_1	-0.5630275	.	0	265.6981737879304	0	1.0	0	180	0	180	780.0186987409819	324	324	1.0	0.0	0.340630518494993	0.340630518494993
+    chr1	6200000	7300000	ID_0.01_2	-0.235798	.	288.00513572726237	327.503479611623	1.0	1.0	198	231	198	231	339.91508704783513	121	121	1.0	0.8472855330682405	0.9634861531331044	1.8107716862013452
+    chr1	7300000	9500000	ID_0.01_3	-0.44334	.	340.12385944568155	159.40880484157745	1.0	1.0	242	110	242	110	1078.1133262629996	484	484	1.0	0.31548061892958207	0.14785904316211984	0.46333966209170185
+    chr1	9500000	10100000	ID_0.01_4	-1.021538	.	186.65816676710497	124.2235190772146	1.0	1.0	132	84	132	84	118.58286349492002	36	36	1.0	1.5740737005823884	1.0475672067282826	2.6216409073106712
+
+
+
+.. image:: ../../images/ratio.png

docs/index.rst

@@ -66,6 +66,8 @@ tool                                 description
 :ref:`hicPlotSVL`                    Computing short vs long range contacts and plotting the results
 :ref:`hicHyperoptDetectLoops`        Search for optimal hicDectectLoops parameters
 :ref:`hicHyperoptDetectLoopsHiCCUPS` Search for optimal Juicer HiCCUPS parameters
+:ref:`hicInterIntraTAD`              Extras and computes inter and intra TAD data
+
 ==================================== ==========================================================================================================================================================
 
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