Merge pull request #315 from deeptools/develop

Release 3.6
deeptools · Nov 12, 2020 · ce2ec50 · ce2ec50
2 parents 1c6b592 + 5f0353b
commit ce2ec50
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diff --git a/.gitignore b/.gitignore
@@ -24,7 +24,7 @@ lib64
 pip-log.txt
 
 # Unit test / coverage reports
-.coverage
+.coverage*
 .tox
 nosetests.xml
 htmlcov

diff --git a/.travis.yml b/.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:

diff --git a/README.md b/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
 -------------
 

diff --git a/docs/conf.py b/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()

diff --git a/docs/content/all_default_properties_rst.txt b/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                      
 =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================  =============================
 
 

diff --git a/docs/content/citation.rst b/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.
diff --git a/docs/content/images/graphicalabstract.png b/docs/content/images/graphicalabstract.png
diff --git a/docs/content/installation.rst b/docs/content/installation.rst
@@ -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

diff --git a/docs/content/releases.rst b/docs/content/releases.rst
@@ -4,6 +4,7 @@ Releases
 .. toctree::
    :maxdepth: 1
 
+   releases/3.6
    releases/3.5.1
    releases/3.5
    releases/3.4

diff --git a/docs/content/releases/3.6.rst b/docs/content/releases/3.6.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.
diff --git a/docs/content/tracks/auto/bedgraph_matrix_options_text.txt b/docs/content/tracks/auto/bedgraph_matrix_options_text.txt
@@ -29,7 +29,7 @@ type = lines
 # the default color map is viridis
 # If you want your own colormap you can put the values of the color you want
 # For example, colormap = ['blue', 'yellow', 'red']
-# or colormap = ['white', (1, 0.88, 2./3), (1, 0.74, 0.25), (1, 0.5, 0), (1, 0.19, 0), (0.74, 0, 0), (0.35, 0, 0)]
+# or colormap = ['white', (1, 0.88, .66), (1, 0.74, 0.25), (1, 0.5, 0), (1, 0.19, 0), (0.74, 0, 0), (0.35, 0, 0)]
 #colormap = Reds
 # pos_score_in_bin means 'position of score with respect to bin start and end'
 # if the lines option is used, the y values can be put at the

diff --git a/docs/content/tracks/auto/hic_matrix_options_text.txt b/docs/content/tracks/auto/hic_matrix_options_text.txt
@@ -4,7 +4,7 @@
 # the default color map is RdYlBu_r (_r) stands for reverse
 # If you want your own colormap you can put the values of the color you want
 # For example, colormap = ['blue', 'yellow', 'red']
-# or colormap = ['white', (1, 0.88, 2./3), (1, 0.74, 0.25), (1, 0.5, 0), (1, 0.19, 0), (0.74, 0, 0), (0.35, 0, 0)]
+# or colormap = ['white', (1, 0.88, .66), (1, 0.74, 0.25), (1, 0.5, 0), (1, 0.19, 0), (0.74, 0, 0), (0.35, 0, 0)]
 #colormap = RdYlBu_r
 # depth is the maximum distance that should be plotted.
 # If it is more than 125% of the plotted region, it will

diff --git a/docs/content/tracks/auto/scalebar_deduced_from_code.txt b/docs/content/tracks/auto/scalebar_deduced_from_code.txt
@@ -22,3 +22,7 @@ Optional:
 
 - **size**: by default this option is not set but you can also put: any integer above 0
 
+- **scalebar_start_position**: by default this option is not set but you can also put: any integer above 0
+
+- **scalebar_end_position**: by default this option is not set but you can also put: any integer above 0
+
diff --git a/docs/content/tracks/auto/scalebar_options_text.txt b/docs/content/tracks/auto/scalebar_options_text.txt
@@ -17,14 +17,23 @@ color = black
 # alpha = 0.5
 # line width:
 # line_width = 0.5
+# To set the position and the size of the scale bar
+# 4 parameters can be set:
+# x_center, scalebar_start_position, scalebar_end_position, size
+# scalebar_start_position need to be smaller than x_center smaller than scalebar_end_position
 # x_center: coordinate where the scale bar should be plotted (center)
-# if not set it will be in the middle of the plotted area
+# if not set and cannot be deduce from other parameters
+# it will be in the middle of the plotted area
 #x_center = 3100000
 # size: in bp the length of the scale bar
-# if not set it will be like in UCSC:
+# if not set and cannot be deduced from other parameters
+# it will be like in UCSC:
 # the higher number that begins with 1, 2 or 5 followed by 0s
 # that is less than half the plotted area
 #size = 100000
+# Another example:
+#scalebar_start_position = 2900000
+#scalebar_end_position = 3100000
 # where: where the size of the scale bar should
 # appear among left, right, top, bottom
 # default is left

diff --git a/docs/coverage.svg b/docs/coverage.svg
diff --git a/docs/index.rst b/docs/index.rst
@@ -20,6 +20,10 @@ are highly customizable. Currently, it is possible to plot:
 - links
 - 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>`_):
+
+.. image:: 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>`_.
 

diff --git a/environment.yml b/environment.yml
@@ -7,7 +7,7 @@ channels:
    - conda-forge
 dependencies:
     - numpy >=1.16
-    - matplotlib =3.1.1
+    - matplotlib >=3.1.1,<=3.2.2
     - intervaltree >=2.1.0
     - pybigwig >=0.3.16
     - future >=0.17.0

diff --git a/pygenometracks/_version.py b/pygenometracks/_version.py
@@ -2,4 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-__version__ = '3.5.1'
+__version__ = '3.6'
diff --git a/pygenometracks/plotTracks.py b/pygenometracks/plotTracks.py
@@ -155,9 +155,12 @@
 def parse_arguments(args=None):
     parser = argparse.ArgumentParser(
         description='Plots genomic tracks on specified region(s). '
-                    'Citation : Ramirez et al.  High-resolution TADs reveal DNA '
+                    'Citations :\nRamirez et al.  High-resolution TADs reveal DNA '
                     'sequences underlying genome organization in flies. '
-                    'Nature Communications (2018) doi:10.1038/s41467-017-02525-w',
+                    'Nature Communications (2018) doi:10.1038/s41467-017-02525-w\n'
+                    'Lopez-Delisle et al.  pyGenomeTracks: reproducible'
+                    ' plots for multivariate genomic datasets. '
+                    'Bioinformatics (2020) doi:10.1093/bioinformatics/btaa692',
         usage="%(prog)s --tracks tracks.ini --region chr1:1000000-4000000 -o image.png")
 
     parser.add_argument('--tracks',
@@ -179,10 +182,15 @@ def parse_arguments(args=None):
                        type=argparse.FileType('r')
                        )
 
-    parser.add_argument('--width',
-                        help=f'figure width in centimeters (default is {DEFAULT_FIGURE_WIDTH})',
-                        type=float,
-                        default=DEFAULT_FIGURE_WIDTH)
+    width_group = parser.add_mutually_exclusive_group()
+    width_group.add_argument('--width',
+                             help=f'figure width in centimeters (default is {DEFAULT_FIGURE_WIDTH})',
+                             type=float,
+                             default=DEFAULT_FIGURE_WIDTH)
+    width_group.add_argument('--plotWidth',
+                             help='width in centimeters of the plotting (central) part',
+                             type=float,
+                             default=None)
 
     parser.add_argument('--height',
                         help='Figure height in centimeters. If not given, the figure height is computed '
@@ -310,7 +318,7 @@ def main(args=None):
     trp = PlotTracks(args.tracks.name, args.width, fig_height=args.height,
                      fontsize=args.fontSize, dpi=args.dpi,
                      track_label_width=args.trackLabelFraction,
-                     plot_regions=regions)
+                     plot_regions=regions, plot_width=args.plotWidth)
 
     # Plot them
     if args.BED:

diff --git a/pygenometracks/tests/generateAllOutput.sh b/pygenometracks/tests/generateAllOutput.sh
@@ -35,6 +35,7 @@ bin/pgt --tracks ./pygenometracks/tests/test_data/operation_bdg.ini --region X:2
 bin/pgt --tracks ./pygenometracks/tests/test_data/bedgraph_withNA.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_bedgraph_withNA.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/bedgraph_negative.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_negative.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/bedgraph_end_not_covered.ini --region chr7:100-400 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_bedgraph_end_not_covered.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/bedgraph_useMid_op.ini --region chr2:74000000-74800000 --trackLabelFraction 0.2 --dpi 130  -o ./pygenometracks/tests/test_data/master_bedgraph_useMid_op.png
 
 # test bigWigTrack:
 bin/pgt --tracks ./pygenometracks/tests/test_data/bigwig.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_bigwig.png
@@ -45,6 +46,10 @@ bin/pgt --tracks ./pygenometracks/tests/test_data/operation.ini --region fakeChr
 bin/pgt --tracks ./pygenometracks/tests/test_data/grid.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_grid.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/example_bigwig.ini --region X:2,500,000-3,000,000 -o ./pygenometracks/tests/test_data/master_example_bigwig.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/example_op.ini --region 2L:0-1000 -o ./pygenometracks/tests/test_data/master_operation_2L.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/example_bigwig.ini --region X:2,500,000-3,000,000 --width 12 -o ./pygenometracks/tests/test_data/master_example_bigwig_width12.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/example_bigwig.ini --region X:2,500,000-3,000,000 --plotWidth 12 -o ./pygenometracks/tests/test_data/master_example_bigwig_plotwidth12.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/example_bigwig.ini --region X:2,500,000-3,000,000 --plotWidth 12 --trackLabelFraction 0.5 -o ./pygenometracks/tests/test_data/master_example_bigwig_plotwidth12Lab0.5.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/example_op2.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_operation_scien.png
 
 # test_epilogosTrack:
 bin/pgt --tracks ./pygenometracks/tests/test_data/epilogos.ini --region X:3100000-3150000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_epilogos.png
@@ -65,6 +70,7 @@ bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic_one_interac
 bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic_one_interaction_cool.ini --region chrY:0-1000000 --trackLabelFraction 0.23 --width 38 -o ./pygenometracks/tests/test_data/master_plot_hic_one_interaction_withRegion_chrY-0-1000000.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic_one_interaction_diag_h5.ini --region chrY:0-1000000 --trackLabelFraction 0.23 --width 38 -o ./pygenometracks/tests/test_data/master_plot_hic_one_interaction_diag_chrY-0-1000000.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic_small_test_3.ini --region chr1:0-200000 --trackLabelFraction 0.23 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_hic_small_test_3.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic_force_scale.ini --region X:2500000-3500000 --trackLabelFraction 0.23 --width 38 --dpi 130 --fontSize 16 -o ./pygenometracks/tests/test_data/master_plot_hic_force_scale.png
 
 # test_logScale:
 bin/pgt --tracks ./pygenometracks/tests/test_data/log1p.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o ./pygenometracks/tests/test_data/master_log1p.png
@@ -106,3 +112,7 @@ bin/pgt --tracks ./pygenometracks/tests/test_data/arcs_no_score.ini --region X:3
 # tests scaleBar
 bin/pgt --tracks pygenometracks/tests/test_data/scale_bar.ini --region X:3200000-3300000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o pygenometracks/tests/test_data/master_scale_bar_zoom.png
 bin/pgt --tracks pygenometracks/tests/test_data/scale_bar.ini --region X:3000000-3300000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o pygenometracks/tests/test_data/master_scale_bar.png
+bin/pgt --tracks pygenometracks/tests/test_data/scale_bar_startend.ini --region X:3000000-3600000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o pygenometracks/tests/test_data/master_scale_bar_startend.png
+bin/pgt --tracks pygenometracks/tests/test_data/scale_bar_startend.ini --region X:3000000-3600000 --trackLabelFraction 0.2 --width 38 --dpi 130 --decreasingXAxis -o pygenometracks/tests/test_data/master_scale_bar_startend_dec.png
+bin/pgt --tracks pygenometracks/tests/test_data/scale_bar_startend.ini --region X:2000000000-2500000000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o pygenometracks/tests/test_data/master_scale_bar_startend_outside.png
+bin/pgt --tracks pygenometracks/tests/test_data/scale_bar_startend.ini --region X:3199500-3201000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o pygenometracks/tests/test_data/master_scale_bar_startend_superzoom.png
diff --git a/pygenometracks/tests/test_bedGraphMatrixTrack.py b/pygenometracks/tests/test_bedGraphMatrixTrack.py
@@ -73,9 +73,9 @@
 
 [test bedgraph matrix]
 file = tad_separation_score.bm.gz
-title = bedgraph matrix (file type is tabix) colormap = Reds
+title = bedgraph matrix (file type is tabix) colormap = pink
 height = 5
-colormap = Reds
+colormap = pink
 file_type = bedgraph_matrix
 
 [spacer]
Original file line number	Diff line number	Diff line change
Expand Up		@@ -22,3 +22,7 @@ Optional:

		- size: by default this option is not set but you can also put: any integer above 0

		- scalebar_start_position: by default this option is not set but you can also put: any integer above 0

		- scalebar_end_position: by default this option is not set but you can also put: any integer above 0