Merge pull request #315 from deeptools/develop

Release 3.6

Author: lldelisle

.gitignore

@@ -24,7 +24,7 @@ lib64
 pip-log.txt
 
 # Unit test / coverage reports
-.coverage
+.coverage*
 .tox
 nosetests.xml
 htmlcov

.travis.yml

@@ -13,11 +13,11 @@ deploy:
   python:
     - 3.6
     - 3.7
-    #- 3.8
+    - 3.8
 env:
 - TRAVIS_PYTHON_VERSION=3.6
 - TRAVIS_PYTHON_VERSION=3.7
-#- TRAVIS_PYTHON_VERSION=3.8
+- TRAVIS_PYTHON_VERSION=3.8
 
 os:
 - linux
@@ -58,7 +58,7 @@ before_install:
 - conda update -q conda
 - conda info -a
 install:
-- conda install --yes -c bioconda -c conda-forge python=$TRAVIS_PYTHON_VERSION --file requirements.txt
+- conda install --yes -c bioconda -c conda-forge python=$TRAVIS_PYTHON_VERSION --file requirements_travis.txt
 - conda install --yes -c conda-forge -c bioconda pytest nose ghostscript pathlib
 - python setup.py install
 script:

README.md

@@ -20,6 +20,10 @@ are highly customizable. Currently, it is possible to plot:
  * links (represented as arcs)
  * Hi-C matrices
 
+Here is a scheme which describe how pyGenomeTracks is working (graphical abstract of [Lopez-Delisle et al. 2020](https://doi.org/10.1093/bioinformatics/btaa692)):
+
+![pyGenomeTracks](./docs/content/images/graphicalabstract.png)
+
 pyGenomeTracks can make plots with or without Hi-C data. The following is an example output of
 pyGenomeTracks from [Ramírez et al. 2017](https://www.nature.com/articles/s41467-017-02525-w)
 
@@ -99,6 +103,8 @@ optional arguments:
                         case, multiple files will be created using a prefix
                         the value of --outFileName
   --width WIDTH         figure width in centimeters (default is 40)
+  --plotWidth PLOTWIDTH
+                        width in centimeters of the plotting (central) part
   --height HEIGHT       Figure height in centimeters. If not given, the figure
                         height is computed based on the heights of the tracks.
                         If given, the track height are proportionally scaled
@@ -129,10 +135,13 @@ optional arguments:
 
 Citation
 ---------
-If you use pyGenomeTracks in your analysis, you can cite the following paper :
+If you use pyGenomeTracks in your analysis, you can cite the following papers:
 
 Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A. Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar & Thomas Manke. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nature Communications (2018) [doi:10.1038/s41467-017-02525-w](https://www.nature.com/articles/s41467-017-02525-w)
 
+Lopez-Delisle L, Rabbani L, Wolff J, Bhardwaj V, Backofen R, Grüning B, Ramírez F, Manke T. pyGenomeTracks: reproducible plots for multivariate genomic data sets. Bioinformatics. 2020 Aug 3:btaa692. [doi: 10.1093/bioinformatics/btaa692](https://doi.org/10.1093/bioinformatics/btaa692). Epub ahead of print. PMID: 32745185.
+
+
 Documentation
 -------------
 

docs/conf.py

@@ -29,7 +29,8 @@
                 # For plotTracks in utilities
                 'numpy',
                 'tqdm',
-                'intervaltree']
+                'intervaltree',
+                'pybedtools']
 
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()

docs/content/all_default_properties_rst.txt

@@ -56,6 +56,8 @@ show_masked_bins
 scale_factor                                                                                                                                                                                                                                                                                                                                                                        1                                                           
 x_center                                                                                                                                                                                                                                                                                                                                                                                                           not set                      
 size                                                                                                                                                                                                                                                                                                                                                                                                               not set                      
+scalebar_start_position                                                                                                                                                                                                                                                                                                                                                                                            not set                      
+scalebar_end_position                                                                                                                                                                                                                                                                                                                                                                                              not set                      
 =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================
 
 

docs/content/citation.rst

@@ -1,6 +1,8 @@
 Citation
 ========
 
-If you use pyGenomeTracks in your analysis, you can cite the following paper :
+If you use pyGenomeTracks in your analysis, you can cite the following papers:
 
 Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn A. Grüning, José Villaveces, Bianca Habermann, Asifa Akhtar & Thomas Manke. High-resolution TADs reveal DNA sequences underlying genome organization in flies. Nature Communications (2018) `doi:10.1038/s41467-017-02525-w <https://www.nature.com/articles/s41467-017-02525-w>`_.
+
+Lopez-Delisle L, Rabbani L, Wolff J, Bhardwaj V, Backofen R, Grüning B, Ramírez F, Manke T. pyGenomeTracks: reproducible plots for multivariate genomic data sets. Bioinformatics. 2020 Aug 3:btaa692. `doi: 10.1093/bioinformatics/btaa692 <https://doi.org/10.1093/bioinformatics/btaa692>`_. Epub ahead of print. PMID: 32745185.

docs/content/images/graphicalabstract.png

@@ -18,7 +18,7 @@ Python dependencies:
 * pyBigWig >= 0.3.16
 * hicmatrix >= 15
 * pysam >= 0.14
-* matplotlib == 3.1.1
+* matplotlib >=3.1.1,<=3.3.2
 * gffutils >= 0.9
 * pybedtools >= 0.8.1
 * tqdm >= 4.20

docs/content/installation.rst

@@ -4,6 +4,7 @@ Releases
 .. toctree::
    :maxdepth: 1
 
+   releases/3.6
    releases/3.5.1
    releases/3.5
    releases/3.4

docs/content/releases.rst

@@ -0,0 +1,34 @@
+3.6
+===
+
+
+Enhancements:
+^^^^^^^^^^^^^
+
+- A new parameter for pyGenomeTracks allow to fix the width of the central part: ``--plotWidth``
+
+- For scale bars, you can now define the position using 2 parameters among ``x_center``, ``size``, ``scalebar_start_position`` and ``scalebar_end_position``.
+
+
+Python dependency with conda:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- Using conda which is the way we recommand installation it is now possible to use Python 3.8.
+
+Relax version control on matplotlib:
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- Any version of matplotlib from 3.1.1 to 3.3.2 is now accepted.
+
+Bugfixes:
+^^^^^^^^^
+
+- When the ``--fontSize`` parameter was used it happened that the colorbar labels were not corresponding to the colorbar ticks. This bug has been fixed.
+
+- The colormap ``pink`` was not working because it was both the name of a color and a colormap. This bug has been fixed.
+
+- When setting ``min_value``, ``max_value``, if the track was empty these values were ignored. This bug has been fixed.
+
+- When using ``operation`` in bedgraph with a ``second_file``, BEDTools is now used to intersect the second file. ``use_middle`` is now taken into account on the second file.
+
+- Different handling of string evaluation of color, colormap and operation.