trackplot 0.6.1__tar.gz → 0.6.4__tar.gz

{trackplot-0.6.1/trackplot.egg-info → trackplot-0.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: trackplot
-Version: 0.6.1
+Version: 0.6.4
 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-0.6.1 → trackplot-0.6.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "trackplot"
-version = "0.6.1"
+version = "0.6.4"
 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-0.6.1 → trackplot-0.6.4}/trackplot/cli.py

@@ -1214,6 +1214,30 @@ def _add_interval(p, f):
 @optgroup.option(
     "--title", type=click.STRING, default=None, help="Title", show_default=True
 )
+@optgroup.option(
+    "--no-title",
+    type=click.BOOL,
+    is_flag=True,
+    default=False,
+    help="Disable the plot title entirely",
+    show_default=True,
+)
+@optgroup.option(
+    "--no-region-text",
+    type=click.BOOL,
+    is_flag=True,
+    default=False,
+    help="Disable the --event region text on the x-axis ruler",
+    show_default=True,
+)
+@optgroup.option(
+    "--junctions-on-top",
+    type=click.BOOL,
+    is_flag=True,
+    default=False,
+    help="Force all junction arcs to be drawn above the density plot (only effective when --density-by-strand is not set)",
+    show_default=True,
+)
 @optgroup.option(
     "--font", type=click.STRING, default=None, help="Fonts", show_default=True
 )
@@ -1362,6 +1386,10 @@ def main(**kwargs):
         normalize_format=kwargs.get("normalize_format"),
         fill_step=kwargs.get("fill_step", "post"),
         smooth_bin=kwargs["smooth_bin"],
+        title=kwargs["title"],
+        no_title=kwargs["no_title"],
+        no_region_text=kwargs["no_region_text"],
+        junctions_on_top=kwargs["junctions_on_top"],
     )
 
 

{trackplot-0.6.1 → trackplot-0.6.4}/trackplot/plot/coord.py

@@ -134,14 +134,17 @@ def set_x_ticks(
         x_label = f"{x_label}, y axis is {log_trans} transformed"
 
     ax.hlines(y=0, xmin=0, xmax=max(graph_coords), color="black", lw=1)
-    ax.text(
-        x=graph_coords[len(graph_coords) // 2],
-        y=-2.8,
-        s=x_label,
-        fontsize=font_size,
-        ha="center",
-        va="top",
-    )
+
+    no_region_text = kwargs.pop("no_region_text", False)
+    if not no_region_text:
+        ax.text(
+            x=graph_coords[len(graph_coords) // 2],
+            y=-2.8,
+            s=x_label,
+            fontsize=font_size,
+            ha="center",
+            va="top",
+        )
 
     bk = 1
     if not sequence and nx_ticks > 1:

{trackplot-0.6.1 → trackplot-0.6.4}/trackplot/plot/core.py

@@ -986,6 +986,11 @@ class Plot(object):
 
         igv_height_scale = kwargs.get("igv_height_scale")
 
+        # Extract / pop custom params before they flow into downstream **kwargs
+        title = kwargs.pop("title", None)
+        no_title = kwargs.pop("no_title", False)
+        junctions_on_top = kwargs.pop("junctions_on_top", False)
+
         # ====== Phase 1: Load data ======
         self._load_plot_data(n_jobs, *args, **kwargs)
 
@@ -1048,8 +1053,8 @@ class Plot(object):
             else:
                 ax_var = plt.subplot(gs[curr_idx, 0])
 
-            if curr_idx == 0:
-                ax_var.set_title(str(self.region), loc="left")
+            if curr_idx == 0 and not no_title:
+                ax_var.set_title(title or str(self.region), loc="left")
 
             max_y_val_, min_y_val_ = self._resolve_plot_y_limits(
                 p,
@@ -1060,6 +1065,12 @@ 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]}"
@@ -1082,6 +1093,7 @@ class Plot(object):
                             distance_between_label_axis=distance_between_label_axis,
                             raster=raster,
                             fill_step=fill_step,
+                            junctions_on_top=junctions_on_top,
                             **temp_params,
                         )
                         curr_idx += 1
@@ -1097,6 +1109,7 @@ class Plot(object):
                         distance_between_label_axis=distance_between_label_axis,
                         raster=raster,
                         fill_step=fill_step,
+                        junctions_on_top=junctions_on_top,
                         **self.params.get(p, {}),
                     )
             elif p.type == "hic":
@@ -1117,6 +1130,7 @@ class Plot(object):
                     min_used_y_val=min_y_val_,
                     distance_between_label_axis=distance_between_label_axis,
                     raster=raster,
+                    junctions_on_top=junctions_on_top,
                     **self.params.get(p, {}),
                 )
                 curr_idx += 1

{trackplot-0.6.1 → trackplot-0.6.4}/trackplot/plot/limits.py

@@ -26,6 +26,7 @@ def _compute_y_limits(
     density_by_strand: bool = False,
     fill_step: str = "post",
     show_mean_jxn_number: bool = False,
+    junctions_on_top: bool = False,
 ) -> Tuple[float, float]:
     """
     Compute y-axis limits from ReadDepth data, including junction arc extents.
@@ -56,6 +57,13 @@ 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
@@ -112,6 +120,8 @@ def _compute_y_limits(
 
             if density_by_strand:
                 jxn_on_top = jxn.strand == "+"
+            elif junctions_on_top:
+                jxn_on_top = True
             else:
                 jxn_on_top = jxn_idx % 2 == 0
                 if abs(min_used_y_val) < max_used_y_val:
@@ -143,17 +153,27 @@ 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:
         if density_by_strand:
             max_used_y_val = max(abs(min_used_y_val), max_used_y_val)
             min_used_y_val = -max_used_y_val
-    elif not density_by_strand and not jxns:
+    elif not density_by_strand and (junctions_on_top or 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
 
 
@@ -190,4 +210,5 @@ def precompute_y_limits(
         density_by_strand=kwargs.get("density_by_strand", False),
         fill_step=fill_step,
         show_mean_jxn_number=False,
+        junctions_on_top=kwargs.get("junctions_on_top", False),
     )

{trackplot-0.6.1 → trackplot-0.6.4}/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
     )
@@ -490,6 +493,8 @@ def plot_density(
     # Compute y limits using shared logic
     fixed_max_used_y = max_used_y_val is not None
 
+    junctions_on_top = kwargs.get("junctions_on_top", False)
+
     max_used_y_val, min_used_y_val = _compute_y_limits(
         data=data,
         region=region,
@@ -499,8 +504,9 @@ def plot_density(
         density_by_strand=kwargs.get("density_by_strand", False),
         fill_step=fill_step,
         show_mean_jxn_number=show_mean_jxn_number,
+        junctions_on_top=junctions_on_top,
     )
-
+    
     # Draw fill
     x, y1, y2 = [], [], []
     for i in range(len(graph_coords)):
@@ -543,7 +549,7 @@ 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)
             )
@@ -554,6 +560,8 @@ def plot_density(
 
             if kwargs.get("density_by_strand"):
                 jxn_on_top = jxn.strand == "+"
+            elif junctions_on_top:
+                jxn_on_top = True
             else:
                 jxn_on_top = jxn_idx % 2 == 0
                 if abs(min_used_y_val) < max_used_y_val:
@@ -573,6 +581,7 @@ 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)),
@@ -655,7 +664,7 @@ def plot_density(
     ):
         max_used_y_val = max(abs(min_used_y_val), max_used_y_val)
         min_used_y_val = -max_used_y_val
-    elif not kwargs.get("density_by_strand") and not jxns:
+    elif not kwargs.get("density_by_strand") and (junctions_on_top or not jxns):
         min_used_y_val = 0
 
     set_y_ticks(

{trackplot-0.6.1 → trackplot-0.6.4/trackplot.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: trackplot
-Version: 0.6.1
+Version: 0.6.4
 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