Merge pull request #212 from deeptools/fail_proof_hicaggregate

added a hidden parameter to disable "bbox=tight", hoping that this ch…

Author: joachimwolff

hicexplorer/hicAggregateContacts.py

@@ -157,6 +157,10 @@ def parse_arguments(args=None):
                             type=float,
                             default=None)
 
+    #  If set, then the bbox=tight option is disable. Used for automatic testing
+    parserPlot.add_argument('--disable_bbox_tight',
+                            help=argparse.SUPPRESS,
+                            action='store_true')
     return parser
 
 
@@ -407,7 +411,11 @@ def plot_aggregated_contacts(chrom_matrix, chrom_contact_position, cluster_ids,
         cbar_x = plt.subplot(gs[-1, idx])
         fig.colorbar(img, cax=cbar_x, orientation='horizontal')
 
-    plt.savefig(args.outFileName.name, dpi=100, bbox_inches='tight')
+    if args.disable_bbox_tight:
+        plt.savefig(args.outFileName.name, dpi=100)
+    else:
+        plt.savefig(args.outFileName.name, dpi=100, bbox_inches='tight')
+
     plt.close()
 
 

hicexplorer/test/test_data/Li_et_al_2015.cool

@@ -1,14 +1,18 @@
-hicAggregateContacts --matrix ../Li_et_al_2015.cool --BED test_regions.bed \
+hicAggregateContacts --matrix ../Li_et_al_2015.h5 --BED test_regions.bed \
     --outFileName master_aggregate.png \
-    --numberOfBins 30 --range 50000:900000
+    --numberOfBins 30 --range 50000:900000 --disable_bbox_tight
 
-hicAggregateContacts --matrix ../Li_et_al_2015.cool --BED test_regions.bed \
+hicAggregateContacts --matrix ../Li_et_al_2015.h5 --BED test_regions.bed \
     --outFileName master_aggregate_hclust4.png \
     --numberOfBins 30 --range 50000:900000 --hclust 4 \
-    --diagnosticHeatmapFile master_heatmap.png --howToCluster diagonal
+    --diagnosticHeatmapFile master_heatmap.png --howToCluster diagonal --disable_bbox_tight
 
-hicAggregateContacts --matrix ../Li_et_al_2015.cool --BED test_regions.bed \
+hicAggregateContacts --matrix ../Li_et_al_2015.h5 --BED test_regions.bed \
     --outFileName master_aggregate_3d.png \
     --numberOfBins 30 --range 50000:900000 --hclust 2 \
     --plotType 3d \
-    --BED2 test_regions.bed
+    --BED2 test_regions.bed --disable_bbox_tight
+
+hicAggregateContacts --matrix ../Li_et_al_2015.cool --BED test_regions.bed \
+    --outFileName master_aggregate_cool.png \
+    --numberOfBins 30 --range 50000:900000 --disable_bbox_tight

hicexplorer/test/test_data/hicAggregateContacts/make_master_images.sh

@@ -28,8 +28,8 @@ def test_hicAggregateContacts():
 
     outfile_aggregate_plots = NamedTemporaryFile(suffix='.png', prefix='hicaggregate_test_', delete=False)
 
-    args = "--matrix {root}/Li_et_al_2015.cool --BED {root}/hicAggregateContacts/test_regions.bed " \
-           "--outFileName {out_agg} --numberOfBins 30 --range 50000:900000".\
+    args = "--matrix {root}/Li_et_al_2015.h5 --BED {root}/hicAggregateContacts/test_regions.bed " \
+           "--outFileName {out_agg} --numberOfBins 30 --range 50000:900000 --disable_bbox_tight ".\
         format(root=ROOT, out_agg=outfile_aggregate_plots.name)
 
     test_image_agg = ROOT + 'hicAggregateContacts/master_aggregate.png'
@@ -42,16 +42,36 @@ def test_hicAggregateContacts():
     os.remove(outfile_aggregate_plots.name)
 
 
+@pytest.mark.skipif(MID_MEMORY > memory,
+                    reason="Travis has too less memory to run it.")
+def test_hicAggregateContacts_cooler():
+
+    outfile_aggregate_plots = NamedTemporaryFile(suffix='.png', prefix='hicaggregate_test_', delete=False)
+
+    args = "--matrix {root}/Li_et_al_2015.cool --BED {root}/hicAggregateContacts/test_regions.bed " \
+           "--outFileName {out_agg} --numberOfBins 30 --range 50000:900000 --disable_bbox_tight ".\
+        format(root=ROOT, out_agg=outfile_aggregate_plots.name)
+
+    test_image_agg = ROOT + 'hicAggregateContacts/master_aggregate_cool.png'
+
+    hicexplorer.hicAggregateContacts.main(args.split())
+
+    res = compare_images(test_image_agg, outfile_aggregate_plots.name, tolerance)
+    assert res is None, res
+
+    os.remove(outfile_aggregate_plots.name)
+
+
 @pytest.mark.skipif(MID_MEMORY > memory,
                     reason="Travis has too less memory to run it.")
 def test_hicAggregateContacts_clustering():
 
     outfile_aggregate_plots = NamedTemporaryFile(suffix='.png', prefix='hicaggregate_test_', delete=False)
     outfile_heatmaps = NamedTemporaryFile(suffix='.png', prefix='hicaggregate_heatmap_', delete=False)
 
-    args = "--matrix {root}/Li_et_al_2015.cool --BED {root}/hicAggregateContacts/test_regions.bed " \
+    args = "--matrix {root}/Li_et_al_2015.h5 --BED {root}/hicAggregateContacts/test_regions.bed " \
            "--outFileName {out_agg} --numberOfBins 30 --range 50000:900000 --hclust 4 " \
-           "--diagnosticHeatmapFile {out_heat} --howToCluster diagonal " \
+           "--diagnosticHeatmapFile {out_heat} --howToCluster diagonal  --disable_bbox_tight " \
            "--BED2 {root}/hicAggregateContacts/test_regions.bed".format(root=ROOT, out_agg=outfile_aggregate_plots.name,
                                                                         out_heat=outfile_heatmaps.name)
 
@@ -76,9 +96,9 @@ def test_hicAggregateContacts_3d():
 
     outfile_aggregate_3d = NamedTemporaryFile(suffix='.png', prefix='hicaggregate_test_3d', delete=False)
 
-    args = "--matrix {root}/Li_et_al_2015.cool --BED {root}/hicAggregateContacts/test_regions.bed " \
+    args = "--matrix {root}/Li_et_al_2015.h5 --BED {root}/hicAggregateContacts/test_regions.bed " \
            "--outFileName {out_agg} --numberOfBins 30 --range 50000:900000 --hclust 2 " \
-           "--plotType 3d " \
+           "--plotType 3d --disable_bbox_tight " \
            "--BED2 {root}/hicAggregateContacts/test_regions.bed".format(root=ROOT, out_agg=outfile_aggregate_3d.name)
 
     test_image_agg_3d = ROOT + 'hicAggregateContacts/master_aggregate_3d.png'