implement graph orientation change (graphviz rankdir) (#289)

doc/md/README_go_plot.md

@@ -114,4 +114,22 @@ scripts/go_plot.py GO:0003304 GO:0003146#d6fffa --r -o heart_jogging_ice_r1.png
 ![heart_jogging_r1](../images/plot_go/heart_jogging_ice_r1.png)
 
 
+## Chage orietation of plot output
+With graphviz, it is possible to change the orientation of the graph output, which may be convenient for large graphs.
+Options are TB, LR, BT and RL mirroring GraphViz ![https://graphviz.org/docs/attrs/rankdir/](https://graphviz.org/docs/attrs/rankdir/)
+
+```
+# top -> bottom (default)
+scripts/go_plot.py GO:0000010 -o orientation_TB.png --obo=tests/data/mini_obo.obo --rankdir=TB
+```
+![TB](../images/plot_go/rankdir_TB.png)
+
+```
+# left -> right
+scripts/go_plot.py GO:0000010 -o orientation_LR.png --obo=tests/data/mini_obo.obo --rankdir=LR
+```
+![LR](../images/plot_go/rankdir_LR.png)
+
+
+
 Copyright (C) 2010-2018, DV Klopfenstein, Haibao Tang et al. All rights reserved.

goatools/cli/gosubdag_plot.py

@@ -17,6 +17,7 @@
              [--draw-children]
              [--norel]
              [--go_color_file=<file.txt>]
+             [--rankdir=<rankdir>]
   go_plot.py [GO ...] [--obo=<file.obo>] [-o <file.png>] [-t <title>]
              [--shorten] [-p] [-c]
   go_plot.py [GO ...] [-o <file.png>] [--draw-children]
@@ -58,6 +59,7 @@
   --draw-children                      Draw children. By default, they are not drawn.
   --go_aliases=<go_aliases.txt>        ASCII file containing letter alias
   --go_color_file=<file.txt>           GO color file. GO and color (eg #cafffb)
+  --rankdir=TB|LR|BT|RL                Choose orientation of graph; Top->Bottom, Left->Right, ... [default: TB]
 
   --norel                              Don't load relationship from the GO DAG
 """
@@ -151,7 +153,9 @@ class PlotCli(object):
                     'obo',
                     'relationships',
                     'go_color_file',
-                    'go_aliases'])
+                    'go_aliases',
+                    'rankdir',
+                    ])
     kws_set = set(['relationship',
                    'parentcnt', 'childcnt', 'mark_alt_id', 'shorten',
                    'draw-children',

goatools/gosubdag/plot/gosubdag_plot.py

@@ -152,6 +152,7 @@ def _init_kws(self, **kws_usr):
             kws_self['dag']['labelloc'] = 't'
         dpi = str(kws_self['dag'].get('dpi', self.dflts['dpi']))
         kws_self['dag']['dpi'] = dpi
+        kws_self['dag']['rankdir'] = kws_usr.get('rankdir', 'TB')
         return kws_self
 
     def plt_dag(self, fout_img, engine="pydot"):

tests/test_go_plot_orient.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+"""Test running go_plot subdag with different output orientation."""
+
+from __future__ import print_function
+
+import os
+import subprocess
+
+
+def cmds_plot_annos():
+    """Test running go_plot subdag with different output orientation."""
+    for idx, (cmd, check) in enumerate(_get_cmds()):
+        print('------------------- TEST {I} ------------------------------------'.format(I=idx))
+        print(f'CMD: {cmd}')
+        r = subprocess.run(cmd, shell=True, cwd='..')
+        assert r.returncode == 0
+
+        with open('bbbb.dot') as f:
+            ff = f.read()
+            if check not in ff:
+                raise AssertionError(f'Expected phrase "{check}" were not found in dot output.')
+        os.remove('bbbb.dot')
+
+        print("TEST PASSED")
+
+
+def _get_cmds():
+    """Commands for generation of different styles, output md5sum"""
+    # pylint: disable=line-too-long
+    return [
+        ('scripts/go_plot.py GO:0000010 -o tests/bbbb.dot --obo=tests/data/mini_obo.obo', 'rankdir=TB'),
+        ('scripts/go_plot.py GO:0000010 -o tests/bbbb.dot --obo=tests/data/mini_obo.obo --rankdir=TB', 'rankdir=TB'),
+        ('scripts/go_plot.py GO:0000010 -o tests/bbbb.dot --obo=tests/data/mini_obo.obo --rankdir=LR', 'rankdir=LR'),
+        ('scripts/go_plot.py GO:0000010 -o tests/bbbb.dot --obo=tests/data/mini_obo.obo --rankdir=BT', 'rankdir=BT'),
+        ('scripts/go_plot.py GO:0000010 -o tests/bbbb.dot --obo=tests/data/mini_obo.obo --rankdir=RL', 'rankdir=RL'),
+    ]
+
+
+if __name__ == '__main__':
+    cmds_plot_annos()