fix genes inverted

docs/content/releases/3.8.rst

@@ -19,6 +19,7 @@ Bugfix:
 - The installation instructions have been updated
 - Fixed a small bug in links track with "use_middle" enabled, where midpoints could have different ordering than start points (Thanks to @Jeff1995 ).
 - Fix a bug when plotting gtf in the middle of a large intron
+- Fix plot genes with ``orientation = inverted``
 
 Relax version control on matplotlib:
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

pygenometracks/tests/generateAllOutput.sh

@@ -23,6 +23,7 @@ bin/pgt --tracks ./pygenometracks/tests/test_data/bed_genes_rgb.ini --region chr
 bin/pgt --tracks ./pygenometracks/tests/test_data/gtf_merge_overlapping_exons.ini --region chr2:74,704,000-74,710,000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_gtf_merge_overlapping_exons.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/gtf_no_exon.ini --region 381:0-1000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_gtf_no_exon.png
 bin/pgt --tracks ./pygenometracks/tests/test_data/gtf_long_intron.ini --region chr4:147085588-147087450 --trackLabelFraction 0.2 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_gtf_long_intron.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/bed_inverted.ini --region chrX:0-2500000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_bed_inverted.png
 
 # non_classical_bed
 bin/pgt --tracks pygenometracks/tests/test_data/bed_unusual_formats.ini --region X:20000-40000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o pygenometracks/tests/test_data/master_bed_unusual_formats.png

pygenometracks/tests/test_bed_and_gtf_tracks.py

@@ -887,6 +887,29 @@
 with open(os.path.join(ROOT, "gtf_long_intron.ini"), 'w') as fh:
  fh.write(browser_tracks)
 
+browser_tracks = """
+[genes 2]
+file = dm3_genes.bed.gz
+height = 7
+title = genes
+
+[spacer]
+height = 0.05
+
+[x-axis]
+where = top
+
+[spacer]
+height = 0.05
+
+[genes 2bis]
+file = dm3_genes.bed.gz
+height = 7
+orientation = inverted
+title = genes orientation = inverted
+"""
+with open(os.path.join(ROOT, "bed_inverted.ini"), 'w') as fh:
+ fh.write(browser_tracks)
 
 tolerance = 13 # default matplotlib pixed difference tolerance
 
@@ -1412,3 +1435,21 @@ def test_plot_gtf_long_intron():
  assert res is None, res
 
  os.remove(outfile.name)
+
+
+def test_bed_inverted():
+
+ outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_',
+ delete=False)
+ ini_file = os.path.join(ROOT, 'bed_inverted.ini')
+ region = "chrX:0-2500000"
+ expected_file = os.path.join(ROOT, 'master_bed_inverted.png')
+ args = f"--tracks {ini_file} --region {region} "\
+ "--trackLabelFraction 0.2 --width 38 --dpi 130 "\
+ f"--outFileName {outfile.name}".split()
+ pygenometracks.plotTracks.main(args)
+ res = compare_images(expected_file,
+ outfile.name, tolerance)
+ assert res is None, res
+
+ os.remove(outfile.name)

pygenometracks/tests/test_data/bed_inverted.ini

@@ -0,0 +1,20 @@
+
+[genes 2]
+file = dm3_genes.bed.gz
+height = 7
+title = genes
+
+[spacer]
+height = 0.05
+
+[x-axis]
+where = top
+
+[spacer]
+height = 0.05
+
+[genes 2bis]
+file = dm3_genes.bed.gz
+height = 7
+orientation = inverted
+title = genes orientation = inverted

pygenometracks/tracks/BedTrack.py

@@ -398,11 +398,7 @@ def plot(self, ax, chrom_region, start_region, end_region):
  self.plot_triangles(ax, genes_overlap)
  elif self.properties['display'] == 'squares':
  self.plot_squares(ax, genes_overlap)
- if self.properties['orientation'] == 'inverted':
- ax.set_ylim(start_region, end_region)
- else:
- ax.set_ylim(end_region, start_region)
-
+ ax.set_ylim(end_region, start_region)
  else:
  self.counter = 0
  self.current_small_relative = self.properties['arrowhead_fraction'] * (end_region - start_region)
@@ -626,6 +622,10 @@ def is_right_to(a, b):
  ax.set_ylim(2 + epsilon, ymax)
  elif self.properties['display'] == 'collapsed':
  ax.set_ylim(1 + epsilon, ymax)
+
+ if self.properties['orientation'] == 'inverted':
+ ylims = ax.get_ylim()
+ ax.set_ylim(ylims[1], ylims[0])
 
  def plot_label(self, label_ax, width_dpi, h_align='left'):
  if h_align == 'left':
@@ -1052,10 +1052,7 @@ def plot_triangles(self, ax, genes_overlap):
  if valid_regions == 0:
  self.log.warning(f"No regions found for section {self.properties['section_name']}.\n")
 
- if self.properties['orientation'] == 'inverted':
- ax.set_ylim(ymax, 0)
- else:
- ax.set_ylim(0, ymax)
+ ax.set_ylim(0, ymax)
 
  def plot_squares(self, ax, genes_overlap):
  """