Merge pull request #451 from lldelisle/new_style_deletion

New display: deletions

docs/content/all_possible_properties.txt

@@ -38,9 +38,7 @@
 
 - **display**:
 
-  - for *bed*: collapsed, triangles, interleaved, stacked, squares
-
-  - for *gtf*: collapsed, triangles, interleaved, stacked
+  - for *bed, gtf*: collapsed, triangles, interleaved, stacked, squares, deletions
 
 - **fontstyle**:
 

docs/content/examples.rst

@@ -89,7 +89,16 @@ The second one display a relatively small region and uses vlines and vhighlight.
 
 Examples with bed and gtf
 -------------------------
-Here is an example to explain the parameters for bed and gtf:
+
+Here are all the possible 'display' options:
+
+.. image:: ../../pygenometracks/tests/test_data/master_bed_displays.png
+
+Here are all possible 'style' options (when display is collapsed, interleaved or stacked:
+
+.. image:: ../../pygenometracks/tests/test_data/master_different_UTR.png
+
+Here is an example to explain the parameters for bed and gtf in stacked display:
 
 .. literalinclude:: ../../pygenometracks/tests/test_data/bed_and_gtf_tracks.ini
     :language: INI

docs/content/releases/3.9.rst

@@ -9,9 +9,11 @@ This version drops support for python 3.7.
 Enhancement:
 ^^^^^^^^^^^^
 
-- New style to display bed: ``exonarrows`` which displays arrows with orientation in the exons.
-- For the UCSC stlyle, the color of arrows on introns in customizable
 - pyGenomeTracks now uses font type 42 for pdf and ps which helps modification with illustrator.
+- New display for bed: ``deletions`` which is helpful when you need to show a deletion with precise coordinates.
+- New style to display bed: ``exonarrows`` which displays arrows with orientation in the exons.
+- For the UCSC stlyle, the color of arrows on introns in customable
+- Do not hesistate to check the updated documentation: `here <https://pygenometracks.readthedocs.io/en/latest/content/examples.html#examples-with-bed-and-gtf>`_
 
 Bugfix:
 ^^^^^^^

docs/content/tracks/auto/bed_deduced_from_code.txt

@@ -32,7 +32,7 @@ Optional:
 
 - **style**: `flybase` (default) or UCSC, tssarrow or exonarrows.
 
-- **display**: `stacked` (default) or collapsed, triangles, interleaved or squares.
+- **display**: `stacked` (default) or collapsed, triangles, interleaved, squares or deletions.
 
 - **max_labels**: `60` (default) or any integer above 0
 

docs/content/tracks/auto/bed_options_text.txt

@@ -32,8 +32,8 @@ color = darkblue
 # the display parameter defines how the bed file is plotted.
 # Default is 'stacked' where regions are plotted on different lines so
 # we can see all regions and all labels.
-# The other options are ['collapsed', 'interleaved', 'triangles', 'squares']
-# These 2 options assume that the regions do not overlap.
+# The other options are ['collapsed', 'interleaved', 'triangles', 'squares', 'deletions']
+# These 2 options assume that the regions do not overlap:
 # `collapsed`: The bed regions are plotted one after the other in one line.
 # `interleaved`: The bed regions are plotted in two lines, first up, then down, then up etc.
 # If the bed file contains the exon
@@ -101,9 +101,13 @@ fontsize = 10
 # for exonarrows, you can choose the proportion between the height of the introns and the one of exon
 # (by default introns are half):
 #height_intron = 0.5
-# The two other display options are really different and no label can be display:
+# The two following display options are really different and no label can be display:
 # `triangles` display each region as a triangle, can be useful to overlay with a hic_matrix
 # `squares` display each region as a square along the diagonal, can be useful to overlay with a hic_matrix_square
+# The last display option do not expect overlapping feature:
+# `deletions` display a line on the plotted region (color can be controlled by color_backbone)
+# and a V shape breaking the line for each region in bed (color can be controled by color)
+# Labels can be displayed on bottom centered on the region
 # optional. If not given is guessed from the file ending.
 file_type = bed
 

docs/content/tracks/auto/gtf_deduced_from_code.txt

@@ -28,7 +28,7 @@ Optional:
 
 - **style**: `flybase` (default) or UCSC, tssarrow or exonarrows.
 
-- **display**: `stacked` (default) or collapsed, triangles or interleaved.
+- **display**: `stacked` (default) or collapsed, triangles, interleaved, squares or deletions.
 
 - **max_labels**: `60` (default) or any integer above 0
 

docs/content/tracks/auto/gtf_options_text.txt

@@ -32,8 +32,8 @@ color = darkblue
 # the display parameter defines how the gtf file is plotted.
 # Default is 'stacked' where regions are plotted on different lines so
 # we can see all regions and all labels.
-# The other options are ['collapsed', 'interleaved', 'triangles', 'squares']
-# These 2 last options assume that the regions do not overlap.
+# The other options are ['collapsed', 'interleaved', 'triangles', 'squares', 'deletions']
+# These 2 last options assume that the regions do not overlap:
 # `collapsed`: The gtf regions are plotted one after the other in one line.
 # `interleaved`: The gtf regions are plotted in two lines, first up, then down, then up etc.
 # style to plot the genes when the display is 'stacked', 'collapsed' or 'interleaved'
@@ -98,9 +98,13 @@ fontsize = 10
 # for exonarrows, you can choose the proportion between the height of the introns and the one of exon
 # (by default introns are half):
 #height_intron = 0.5
-# The two other display options are really different and no label can be display:
+# The two following display options are really different and no label can be display:
 # `triangles` display each region as a triangle, can be useful to overlay with a hic_matrix
 # `squares` display each region as a square along the diagonal, can be useful to overlay with a hic_matrix_square
+# The last display option do not expect overlapping feature:
+# `deletions` display a line on the plotted region (color can be controlled by color_backbone)
+# and a V shape breaking the line for each region in bed (color can be controled by color)
+# Labels can be displayed on bottom centered on the region
 # optional. If not given is guessed from the file ending.
 file_type = gtf
 

pygenometracks/tests/generateAllOutput.sh

@@ -25,6 +25,9 @@ bin/pgt --tracks ./pygenometracks/tests/test_data/gtf_no_exon.ini --region 381:0
 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
 bin/pgt --tracks ./pygenometracks/tests/test_data/bed_exonarrows_tracks.ini --region X:3000000-3300000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_bed_exonarrows.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/bed_deletions.ini --region chr1:0-500000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_bed_deletions.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/bed_deletions.ini --region chr1:0-210000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_bed_deletions_zoom.png
+bin/pgt --tracks ./pygenometracks/tests/test_data/bed_displays.ini --region chrX:960000-1170000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o ./pygenometracks/tests/test_data/master_bed_displays.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

@@ -1008,6 +1008,100 @@
 with open(os.path.join(ROOT, "bed_exonarrows_tracks.ini"), 'w') as fh:
     fh.write(browser_tracks)
 
+browser_tracks = """
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed default
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = deletions
+display = deletions
+height = 1
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = deletions color = red labels = false
+display = deletions
+color = red
+labels = false
+height = 1
+
+[spacer]
+
+[empty deletion]
+file = empty.bed
+display = deletions
+height = 1
+title = no deletion ovelayed with genes
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+overlay_previous = share-y
+display = collapsed
+
+[x-axis]
+"""
+with open(os.path.join(ROOT, "bed_deletions.ini"), 'w') as fh:
+    fh.write(browser_tracks)
+
+browser_tracks = """
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = collapsed
+display = collapsed
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = interleaved
+display = interleaved
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = stacked
+display = stacked
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = triangles
+display = triangles
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = squares
+display = squares
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = deletions
+display = deletions
+height = 1
+
+[x-axis]
+"""
+with open(os.path.join(ROOT, "bed_displays.ini"), 'w') as fh:
+    fh.write(browser_tracks)
+
 tolerance = 13  # default matplotlib pixed difference tolerance
 
 
@@ -1568,3 +1662,42 @@ def test_bed_exonarrows():
     assert res is None, res
 
     os.remove(outfile.name)
+
+
+def test_plot_tracks_bed_deletions():
+    extension = '.png'
+    ini_file = os.path.join(ROOT, "bed_deletions.ini")
+    for region, expected_basename_file in [("chr1:0-500000", "master_bed_deletions"),
+                                           ("chr1:0-210000", "master_bed_deletions_zoom")]:
+        outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_',
+                                     delete=False)
+        args = f"--tracks {ini_file} --region {region} "\
+            "--trackLabelFraction 0.2 --width 38 --dpi 130 "\
+            f"--outFileName {outfile.name}".split()
+        pygenometracks.plotTracks.main(args)
+        output_file = outfile.name
+        expected_file = os.path.join(ROOT, expected_basename_file
+                                     + extension)
+        res = compare_images(expected_file,
+                             output_file, tolerance)
+        assert res is None, res
+
+        os.remove(output_file)
+
+
+def test_plot_tracks_bed_displays():
+
+    outfile = NamedTemporaryFile(suffix='.png', prefix='pyGenomeTracks_test_',
+                                 delete=False)
+    ini_file = os.path.join(ROOT, 'bed_displays.ini')
+    region = "chrX:960000-1170000"
+    expected_file = os.path.join(ROOT, 'master_bed_displays.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_deletions.ini

@@ -0,0 +1,38 @@
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed default
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = deletions
+display = deletions
+height = 1
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = deletions color = red labels = false
+display = deletions
+color = red
+labels = false
+height = 1
+
+[spacer]
+
+[empty deletion]
+file = empty.bed
+display = deletions
+height = 1
+title = no deletion ovelayed with genes
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+overlay_previous = share-y
+display = collapsed
+
+[x-axis]

pygenometracks/tests/test_data/bed_deletions_tracks.ini

@@ -0,0 +1,25 @@
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed default
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = deletions
+display = deletions
+height = 1
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = deletions color = red labels = false
+display = deletions
+color = red
+labels = false
+height = 1
+
+[x-axis]

pygenometracks/tests/test_data/bed_displays.ini

@@ -0,0 +1,48 @@
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = collapsed
+display = collapsed
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = interleaved
+display = interleaved
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = stacked
+display = stacked
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = triangles
+display = triangles
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = squares
+display = squares
+height = 4
+
+[spacer]
+
+[genes]
+file = dm3_genes_withrgbandscore.bed.gz
+title = bed display = deletions
+display = deletions
+height = 1
+
+[x-axis]