trackplot 0.6.0__tar.gz → 0.6.3__tar.gz

{trackplot-0.6.0/trackplot.egg-info → trackplot-0.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: trackplot
-Version: 0.6.0
+Version: 0.6.3
 Summary: The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/
 Author-email: ygidtu <ygidtu@gmail.com>
 License-Expression: BSD-3-Clause

{trackplot-0.6.0 → trackplot-0.6.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "trackplot"
-version = "0.6.0"
+version = "0.6.3"
 description = "The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/"
 authors = [
     { name = "ygidtu", email = "ygidtu@gmail.com" }

{trackplot-0.6.0 → trackplot-0.6.3}/trackplot/file/Bam.py

@@ -366,11 +366,9 @@ class Bam(SingleCell):
 
                 if kept:
                     if k.strand == "+":
-                        spanned_junctions_plus[k] = 1 + spanned_junctions_plus.get(k, v)
+                        spanned_junctions_plus[k] = v
                     elif k.strand == "-":
-                        spanned_junctions_minus[k] = -1 + spanned_junctions_minus.get(
-                            k, v
-                        )
+                        spanned_junctions_minus[k] = v
 
         except IOError as err:
             logger.error("There is no .bam file at {0}".format(self.path))

{trackplot-0.6.0 → trackplot-0.6.3}/trackplot/plot/core.py

@@ -880,7 +880,7 @@ class Plot(object):
                 graph_coords=self.graph_coords,
                 **kwargs,
             )
-            logger.info(f"{_max} {_min}")
+
             if obj.label in same_y_by_groups:
                 key = same_y_by_groups[obj.label]
                 max_used_y_dict[key] = max(_max, max_used_y_dict.get(key, 0))
@@ -1060,6 +1060,12 @@ class Plot(object):
                 same_y_sc=kwargs.get("same_y_sc"),
                 same_y=kwargs.get("same_y"),
             )
+            
+            if max_y_val_ is not None:
+                max_y_val_ *= 1.1
+            
+            if min_y_val_ is not None:
+                min_y_val_ *= 1.1
 
             logger.info(
                 f"plotting {p.type} at idx: {curr_idx} with height_ratio: {height_ratio[curr_idx]}"

{trackplot-0.6.0 → trackplot-0.6.3}/trackplot/plot/limits.py

@@ -56,6 +56,13 @@ def _compute_y_limits(
     if base_max % 2 == 1:
         base_max += 1
 
+    # --- Track whether limits were explicitly provided (from precompute/user) ---
+    # When both are given, they already account for junction expansion, so we
+    # must NOT expand them again — doing so causes non-convergent arc growth
+    # (the arc height computed from the incoming limit is larger than the one
+    # used during precomputation, inflating the limit on every re-calculation).
+    _limits_explicitly_set = max_used_y_val is not None and min_used_y_val is not None
+
     # --- Set initial y-axis limits ---
     if max_used_y_val is None:
         max_used_y_val = base_max
@@ -143,8 +150,13 @@ def _compute_y_limits(
                     -right_dens if not ss2_modified else -right_dens - current_height,
                 ]
 
-            max_used_y_val = max(max_used_y_val, max(pts_y))
-            min_used_y_val = min(min_used_y_val, min(pts_y))
+            # Only expand y-limits for junctions when limits were NOT explicitly
+            # provided.  Explicit limits (from precompute / --same-y) already
+            # account for junction arcs; re-expanding would cause non-convergent
+            # growth because arc heights are recomputed from the incoming limit.
+            if not _limits_explicitly_set:
+                max_used_y_val = max(max_used_y_val, max(pts_y))
+                min_used_y_val = min(min_used_y_val, min(pts_y))
 
     # Strand-aware adjustment
     if not isinstance(data, dict) and data.strand_aware:
@@ -154,6 +166,11 @@ def _compute_y_limits(
     elif not density_by_strand and not jxns:
         min_used_y_val = 0
 
+    # Small expansion so the top / bottom arcs have visual breathing room
+    # and do not appear cramped against the axis edge.
+    max_used_y_val *= 1.1
+    min_used_y_val *= 1.1
+
     return max_used_y_val, min_used_y_val
 
 

{trackplot-0.6.0 → trackplot-0.6.3}/trackplot/plot/render.py

@@ -474,7 +474,10 @@ def plot_density(
         _base_max += 1
 
     # Arc height reference: use the LARGER of (data baseline, incoming y-limit)
-    # so arcs look proportional to the visible axis range (especially in --same-y mode).
+    # so arcs look proportional to the visible axis range (especially in
+    # --same-y / --same-y-sc mode).  If we only used the data baseline, panels
+    # with small data would have tiny arcs hugging the x-axis when a large
+    # global y-limit is shared across panels.
     _arc_ref_max = (
         max(_base_max, max_used_y_val) if max_used_y_val is not None else _base_max
     )
@@ -500,8 +503,7 @@ def plot_density(
         fill_step=fill_step,
         show_mean_jxn_number=show_mean_jxn_number,
     )
-    logger.info(f"precomputed y limits: {max_used_y_val} {min_used_y_val}")
-
+    
     # Draw fill
     x, y1, y2 = [], [], []
     for i in range(len(graph_coords)):
@@ -531,6 +533,8 @@ def plot_density(
         min_junction_count = min(jxns.values()) if jxns else 0
         junction_count_gap = max_junction_count - min_junction_count
 
+        text_objs = []
+
         for jxn_idx, jxn in enumerate(jxns_sorted_list):
             leftss, rightss = jxn.start, jxn.end
             if (
@@ -542,7 +546,7 @@ def plot_density(
                     f"junction {jxn} of {y_label} is out of plotting region, skip"
                 )
                 continue
-
+            
             ss1_idx, ss1_modified = get_limited_index(
                 leftss - region.start, len(graph_coords)
             )
@@ -572,6 +576,7 @@ def plot_density(
                     right_dens + current_height,
                     right_dens if not ss2_modified else right_dens + current_height,
                 ]
+
             else:
                 left_dens, right_dens = (
                     abs(data.curr_min(ss1_idx)),
@@ -619,6 +624,17 @@ def plot_density(
                     backgroundcolor="w",
                 )
                 t.set_bbox(dict(alpha=0))
+                text_objs.append(t)
+
+        if show_junction_number and len(text_objs) > 1:
+            adjust_text(
+                text_objs,
+                ax=ax,
+                force_text=(0.5, 0.5),
+                expand=(1.2, 1.2),
+                arrowprops=None,
+                lim=100,
+            )
 
     if obj and obj.title:
         ax.text(

{trackplot-0.6.0 → trackplot-0.6.3/trackplot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: trackplot
-Version: 0.6.0
+Version: 0.6.3
 Summary: The trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets. https://sashimi.readthedocs.io/
 Author-email: ygidtu <ygidtu@gmail.com>
 License-Expression: BSD-3-Clause