Merge branch 'develop' of https://github.com/deeptools/pyGenomeTracks …

…into pRegionForAll

pygenometracks/tests/generateAllOutput.sh

@@ -40,6 +40,8 @@ bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic.ini --regio
 bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic_small_test.ini --BED ./pygenometracks/tests/test_data/regions_chr1XY.bed --trackLabelFraction 0.23 --width 38 -o ./pygenometracks/tests/test_data/master_plot_hic_small_test.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic_small_test.ini --region 1:0-200000 --trackLabelFraction 0.23 --width 38 -o ./pygenometracks/tests/test_data/master_plot_hic_small_test.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic_small_test.ini --region chrM:0-20000 --trackLabelFraction 0.23 --width 38 -o ./pygenometracks/tests/test_data/master_plot_hic_small_test_chrM.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic_small_test.ini --region chr1:0-5000 --trackLabelFraction 0.23 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_hic_small_test_small_region.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/browser_tracks_hic_small_test_2.ini --region chr1:0-100000 --trackLabelFraction 0.23 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_hic_small_test_2.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

pygenometracks/tests/test_data/browser_tracks_hic_small_test_2.ini

@@ -0,0 +1,9 @@
+
+[hic matrix]
+file = small_test2.cool
+title = cool with few interactions depth=10kb
+file_type = hic_matrix
+depth = 10000
+
+
+[x-axis]

pygenometracks/tests/test_hiCMatrixTracks.py

@@ -210,6 +210,20 @@
 with open(os.path.join(ROOT, "browser_tracks_hic_log-log.ini"), 'w') as fh:
     fh.write(browser_tracks_with_hic)
 
+browser_tracks_with_hic_small_2 = """
+[hic matrix]
+file = small_test2.cool
+title = cool with few interactions depth=10kb
+file_type = hic_matrix
+depth = 10000
+
+
+[x-axis]
+"""
+
+with open(os.path.join(ROOT, "browser_tracks_hic_small_test_2.ini"), 'w') as fh:
+    fh.write(browser_tracks_with_hic_small_2)
+
 tolerance = 13  # default matplotlib pixed difference tolerance
 
 
@@ -420,3 +434,39 @@ def test_plot_tracks_with_hic_small_above_chr_length():
     assert res is None, res
 
     os.remove(outfile.name)
+
+
+def test_plot_hic_depth_smaller_binsize():
+
+    outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_',
+                                 delete=False)
+    args = "--tracks {0} --region chr1:0-100000 "\
+           "--trackLabelFraction 0.23 --width 38 " \
+           "--dpi 130 --outFileName {1}" \
+           "".format(os.path.join(ROOT, 'browser_tracks_hic_small_test_2.ini'),
+                     outfile.name).split()
+    pygenometracks.plotTracks.main(args)
+    res = compare_images(os.path.join(ROOT, 'master_hic_small_test_2.png'),
+                         outfile.name, tolerance)
+    print("saving test to {}".format(outfile.name))
+    assert res is None, res
+
+    os.remove(outfile.name)
+
+
+def test_plot_hic_plotting_region_smaller_binsize():
+
+    outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_',
+                                 delete=False)
+    args = "--tracks {0} --region chr1:0-5000 "\
+           "--trackLabelFraction 0.23 --width 38 " \
+           "--dpi 130 --outFileName {1}" \
+           "".format(os.path.join(ROOT, 'browser_tracks_hic_small_test.ini'),
+                     outfile.name).split()
+    pygenometracks.plotTracks.main(args)
+    res = compare_images(os.path.join(ROOT, 'master_hic_small_test_small_region.png'),
+                         outfile.name, tolerance)
+    print("saving test to {}".format(outfile.name))
+    assert res is None, res
+
+    os.remove(outfile.name)

pygenometracks/tracks/HiCMatrixTrack.py

@@ -187,7 +187,9 @@ def set_properties_defaults(self):
 
         self.hic_ma.cut_intervals = new_intervals
         binsize = self.hic_ma.getBinSize()
-        max_depth_in_bins = int(self.properties['depth'] / binsize)
+        # Need to be sure that you keep at least one bin even if the depth is
+        # smaller than the binsize
+        max_depth_in_bins = max(1, int(self.properties['depth'] / binsize))
 
         # work only with the lower matrix
         # and remove all pixels that are beyond
@@ -273,7 +275,9 @@ def plot(self, ax, chrom_region, region_start, region_end):
 
         region_len = region_end - region_start
         depth = min(self.properties['depth'], int(region_len * 1.25))
-        depth_in_bins = int(1.5 * region_len / self.hic_ma.getBinSize())
+        # Need to be sure that you keep at least one bin even if the depth is
+        # smaller than the binsize
+        depth_in_bins = max(1, int(1.5 * region_len / self.hic_ma.getBinSize()))
 
         if depth < self.properties['depth']:
             log.warning("The depth was set to {} which is more than 125%"
@@ -316,12 +320,13 @@ def plot(self, ax, chrom_region, region_start, region_end):
             vmin = self.properties['min_value']
         else:
             if depth_in_bins > matrix.shape[0]:
-                depth_in_bins = matrix.shape[0] - 5
+                # Make sure you keep one bin
+                depth_in_bins = max(1, matrix.shape[0] - 5)
 
             # if the region length is large with respect to the chromosome length, the diagonal may have
             # very few values or none. Thus, the following lines reduce the number of bins until the
-            # diagonal is at least length 5
-            num_bins_from_diagonal = int(region_len / self.hic_ma.getBinSize())
+            # diagonal is at least length 5 but make sure you have at least one value:
+            num_bins_from_diagonal = max(1, int(region_len / self.hic_ma.getBinSize()))
             for num_bins in range(0, num_bins_from_diagonal)[::-1]:
                 distant_diagonal_values = matrix.diagonal(num_bins)
                 if len(distant_diagonal_values) > 5: