Small improvements 0003

alldata/bblab_site/tools/isoforms_plot/index.html

@@ -206,15 +206,14 @@
 		}
 
 		.results-section {
-			background: white;
+			background: #fafafa;
 			padding: 30px;
 			margin: 40px auto 30px auto;
 			box-shadow: 0 4px 20px rgba(86, 171, 47, 0.15);
 			border: 2px solid #56ab2f;
 			border-radius: 12px;
 			/* Wider than normal sections but scales with zoom */
-			width: calc(80% - 40px);
-			max-width: 1800px;
+			width: calc(min(1800px, max(80% - 40px, 900px)));
 		}
 
 		.results-section h2 {
@@ -226,12 +225,11 @@
 		}
 
 		.results-content-wrapper {
-			max-width: 900px;
 			margin: 0 auto;
 		}
 
 		.plot-container {
-			background: #fafafa;
+			background: white;
 			padding: 15px;
 			margin: 20px;
 			text-align: center;

alldata/bblab_site/tools/isoforms_plot/isoforms_plot/compiler.py

@@ -6,7 +6,7 @@
 - resolve "end" (None) to END_POS
 """
 
-from collections import Counter
+from collections import Counter, defaultdict
 from dataclasses import dataclass
 from typing import Literal, Optional, Sequence, Tuple
 
@@ -164,14 +164,18 @@ def compile_transcripts(
     # Build groups structure
     # Preserve order of first appearance
     groups_order = []
-    seen = set()
+    group_counts = defaultdict(int)
+    last_group = None
+    last_group_count = 0
     for transcript in parsed_transcripts:
-        if transcript.group not in seen:
+        if transcript.group != last_group:
+            group_counts[last_group] = last_group_count
+            last_group = transcript.group
             groups_order.append(transcript.group)
-            seen.add(transcript.group)
+            last_group_count = 0
+        last_group_count += 1
 
-    # Count transcripts per group
-    group_counts = Counter(t.group for t in parsed_transcripts)
+    group_counts[last_group] = last_group_count  # for the final group
 
     # Build groups list
     compiled_groups = [

alldata/bblab_site/tools/isoforms_plot/isoforms_plot/plotter.py

@@ -624,54 +624,7 @@ def plot(transcripts, groups, splicing_sites, title=None) -> draw.Drawing:
     if lineheight > 5:
         lineheight = 5
 
-    # Calculate total height of all groups for dotted lines
-    # First, we need to determine the height of each group
-    total_groups_height = 0.0
-    transcript_index = 0
-    for group in groups:
-        group_size = group.size
-
-        # Calculate height for this group
-        group_height = 0.0
-        for i in range(group_size):
-            if transcript_index >= len(transcripts):
-                break
-            transcript = transcripts[transcript_index]
-            label = transcript.label
-
-            if i > 0:
-                group_height += 3  # gap between transcripts
-            if label:
-                group_height += lineheight + 9 + 6  # 9 is font_size from GroupWithTranscripts
-            else:
-                group_height += lineheight
-
-            transcript_index += 1
-
-        # Add group height
-        total_groups_height += group_height
-
-    # Add initial gap and extra padding
-    total_groups_height += 30 + 25 + 50  # 25 is initial gap, 50 is extra padding
-
-    # Add title at the top if title is not None
-    if title is not None:
-        figure.add(Title(title), gap=10)
-
-    # add genome overview at the top of the figure so it appears above sample tracks
-    add_genome_overview(figure, LANDMARKS)
-    # add splicing sites display below the genome overview with calculated height
-    figure.add(SplicingSites(splicing_sites, total_samples=total_samples, lineheight=lineheight,
-                            total_height=total_groups_height), gap=5)
-    # add a small blank multitrack to create vertical separation between the splicing sites
-    # and the sample tracks (gap value tuned to avoid overlap with multi-level labels)
-    try:
-        figure.add(Multitrack([Track(START_POS + XOFFSET, START_POS + XOFFSET, color='#ffffff', h=2)]), gap=25)
-    except TypeError:
-        # fallback if Track signature differs; attempt without named color
-        figure.add(Multitrack([Track(START_POS + XOFFSET, START_POS + XOFFSET, color='#ffffff', h=2)]), gap=25)
-
-    # Draw each transcript from transcripts variable, organized by groups
+    # Build all group components first to get their exact heights
     default_color = 'grey'
     max_comment_width = 0.0
     comment_font_size = 8
@@ -680,7 +633,8 @@ def plot(transcripts, groups, splicing_sites, title=None) -> draw.Drawing:
     if aggregate_group_size != len(transcripts):
         raise RuntimeError(f"Bad group sizes: {aggregate_group_size} != {len(transcripts)}")
 
-    transcript_index = 0  # Track position in transcripts list
+    transcript_index = 0
+    group_components = []
 
     for group in groups:
         group_name = group.name
@@ -706,8 +660,48 @@ def plot(transcripts, groups, splicing_sites, title=None) -> draw.Drawing:
             transcripts_data.insert(0, (parts, color, label, comment))
             transcript_index += 1
 
-        # Create and add the group component (contains vertical line and all transcripts)
+        # Create the group component
         group_component = GroupWithTranscripts(group_name, transcripts_data, lineheight=lineheight)
+        group_components.append(group_component)
+
+    # Calculate total height for dotted lines using actual component heights
+    # Dotted lines start at the baseline (line_y) within SplicingSites component
+    # and extend downward through all components that come after
+    total_dotted_height = 0.0
+
+    # Gap after SplicingSites
+    total_dotted_height += 5
+
+    # Multitrack spacer (gap + height)
+    total_dotted_height += 25  # gap before multitrack
+    total_dotted_height += 2   # multitrack height
+
+    # Add all group heights and their gaps
+    for i, group_comp in enumerate(group_components):
+        total_dotted_height += 30  # gap before each group
+        total_dotted_height += group_comp.h  # actual height of the group
+
+    total_dotted_height += 1  # extra padding at the bottom to ensure lines extend beyond last group
+
+    # Add title at the top if title is not None
+    if title is not None:
+        figure.add(Title(title), gap=10)
+
+    # add genome overview at the top of the figure so it appears above sample tracks
+    add_genome_overview(figure, LANDMARKS)
+    # add splicing sites display below the genome overview with calculated height
+    figure.add(SplicingSites(splicing_sites, total_samples=total_samples, lineheight=lineheight,
+                            total_height=total_dotted_height), gap=5)
+    # add a small blank multitrack to create vertical separation between the splicing sites
+    # and the sample tracks (gap value tuned to avoid overlap with multi-level labels)
+    try:
+        figure.add(Multitrack([Track(START_POS + XOFFSET, START_POS + XOFFSET, color='#ffffff', h=2)]), gap=25)
+    except TypeError:
+        # fallback if Track signature differs; attempt without named color
+        figure.add(Multitrack([Track(START_POS + XOFFSET, START_POS + XOFFSET, color='#ffffff', h=2)]), gap=25)
+
+    # Add all pre-created group components to the figure
+    for group_component in group_components:
         figure.add(group_component, gap=30)
 
     # Calculate figure width to accommodate comments

alldata/bblab_site/tools/isoforms_plot/test_isoforms.csv

@@ -4,13 +4,13 @@ My Isoforms Plot Title
 
 [transcripts]
 fragments,label,comment,group
-1-743; 4913-end,vif,(3),My Group 1
-1-743; 5390-end,vpr,(15),My Group 1
-1-743; 4913-4962; 5390-end,vpr,(4),My Group 1
-1-743; 5390-5463; 5976-end,vpu/env,(4),My Group 1
-1-743; 5976-end,vpu/env,(1),My Group 1
-1-743; 4913-4962; 5390-5463; 5976-end,vpu/env,(1),My Group 1
-1-743; 5390-5463; 5976-6046; 8369-end,nef,(14),My Group 1
+1-743; 4913-end,vif,(3),My First Group
+1-743; 5390-end,vpr,(15),My First Group
+1-743; 4913-4962; 5390-end,vpr,(4),My First Group
+1-743; 5390-5463; 5976-end,vpu/env,(4),My First Group
+1-743; 5976-end,vpu/env,(1),My First Group
+1-743; 4913-4962; 5390-5463; 5976-end,vpu/env,(1),My First Group
+1-743; 5390-5463; 5976-6046; 8369-end,nef,(14),My First Group
 1-743; 4913-4962; 5390-5463; 5976-6046; 8369-end,nef,(7)
 1-743; 5976-6046; 8369-end,nef,(6)
 1-710; 5976-6046; 8369-end,nef,(2)