Fix white-line bug in colorbar

Co-authored-by: Copilot <copilot@github.com>

Author: DingWB

PyComplexHeatmap/clustermap.py

@@ -139,11 +139,16 @@ def _determine_cmap_params(self, plot_data, vmin, vmax, cmap, center, robust):
 				vmin = np.nanpercentile(calc_data, 2)
 			else:
 				vmin = np.nanmin(calc_data)
+			# Round to align colorbar QuadMesh boundary with the cax pixel
+			# grid; avoids sub-pixel seams that PDF viewers render as white
+			# lines (matplotlib issue #1188).
+			vmin = round(float(vmin), 2)
 		if vmax is None:
 			if robust:
 				vmax = np.nanpercentile(calc_data, 98)
 			else:
 				vmax = np.nanmax(calc_data)
+			vmax = round(float(vmax), 2)
 		self.vmin, self.vmax = vmin, vmax
 
 		# Choose default colormaps if not provided
@@ -361,7 +366,10 @@ def plot(
 		# Possibly add a colorbar
 		if self.cbar:
 			cb = ax.figure.colorbar(mesh, cax, ax, **self.cbar_kws)
-			cb.outline.set_linewidth(0)
+			# cb.outline.set_linewidth(0)
+			# Hide the sub-pixel seams between QuadMesh cells that PDF/SVG
+			# viewers render as thin white lines (matplotlib issue #1188).
+			cb.solids.set_edgecolor("face")
 			# If rasterized is passed to pcolormesh, also rasterize the
 			# colorbar to avoid white lines on the PDF rendering
 			if kws.get("rasterized", False):
@@ -609,11 +617,16 @@ def plot_heatmap(
 			vmin = np.nanpercentile(calc_data, 2)
 		else:
 			vmin = np.nanmin(calc_data)
+		# Round to align colorbar QuadMesh boundary with the cax pixel grid;
+		# avoids sub-pixel seams that PDF viewers render as white lines
+		# (matplotlib issue #1188).
+		vmin = round(float(vmin), 2)
 	if vmax is None:
 		if robust:
 			vmax = np.nanpercentile(calc_data, 98)
 		else:
 			vmax = np.nanmax(calc_data)
+		vmax = round(float(vmax), 2)
 
 	cmap=adjust_cmap(cmap,vmin=vmin,vmax=vmax,center=center,
 					 na_col=na_col)
@@ -2311,7 +2324,7 @@ def collect_legends(self):
 			self.legend_kws.setdefault("vmin", self.kwargs.get('vmin')) #round(vmin, 2))
 			self.legend_kws.setdefault("vmax", self.kwargs.get('vmax')) #round(vmax, 2))
 			self.legend_kws.setdefault("center", self.kwargs.get('center', None))
-			self.legend_kws.setdefault("extend", 'both')
+			self.legend_kws.setdefault("extend", 'both') # 'neither', 'both', 'min', 'max'
 			self.legend_kws.setdefault("extendfrac", 0.15)
 			cbar_height=self.legend_kws.pop('cbar_height',20)
 			self.legend_dict[self.label]=tuple([self.cmap, self.label, self.legend_kws, cbar_height, "cmap"])

PyComplexHeatmap/dotHeatmap.py

@@ -440,10 +440,13 @@ def format_data(self, data, mask=None, z_score=None, standard_scale=None):
 				self.kwargs["marker"] = self.marker
 
 		if 'vmin' not in self.kwargs:
-			self.vmin = np.nanmin(data2d.values)
+			# Round to align the colorbar QuadMesh boundary with the cax pixel
+			# grid; avoids sub-pixel seams that PDF viewers render as white
+			# lines (matplotlib issue #1188).
+			self.vmin = round(float(np.nanmin(data2d.values)), 2)
 			self.kwargs.setdefault("vmin", self.vmin)
 		if 'vmax' not in self.kwargs:
-			self.vmax = np.nanmax(data2d.values)
+			self.vmax = round(float(np.nanmax(data2d.values)), 2)
 			self.kwargs.setdefault("vmax", self.vmax)
 
 		if z_score is not None and standard_scale is not None:
@@ -596,8 +599,10 @@ def collect_legends(self):
 
 				if isinstance(self.cmap, dict):  #
 					cmap_legend_kws = self.cmap_legend_kws.copy()
-					cmap_legend_kws.setdefault("vmin", self.kwargs.get('vmin'))  # round(vmin, 2))
-					cmap_legend_kws.setdefault("vmax", self.kwargs.get('vmax'))  # round(vmax, 2))
+					_vmin = self.kwargs.get('vmin')
+					_vmax = self.kwargs.get('vmax')
+					cmap_legend_kws.setdefault("vmin", round(_vmin, 2) if _vmin is not None else _vmin)
+					cmap_legend_kws.setdefault("vmax", round(_vmax, 2) if _vmax is not None else _vmax)
 					cmap_legend_kws.setdefault("center", self.kwargs.get('center', None))
 					cmap_legend_kws.setdefault("extend", 'both')
 					cmap_legend_kws.setdefault("extendfrac", 0.15)
@@ -608,8 +613,10 @@ def collect_legends(self):
 				cmap = self.cmap
 				c = self.kwargs.get("c", None)
 				cmap_legend_kws = self.cmap_legend_kws.copy()
-				cmap_legend_kws.setdefault("vmin", self.kwargs.get('vmin'))  # round(vmin, 2))
-				cmap_legend_kws.setdefault("vmax", self.kwargs.get('vmax'))  # round(vmax, 2))
+				_vmin = self.kwargs.get('vmin')
+				_vmax = self.kwargs.get('vmax')
+				cmap_legend_kws.setdefault("vmin", round(_vmin, 2) if _vmin is not None else _vmin)
+				cmap_legend_kws.setdefault("vmax", round(_vmax, 2) if _vmax is not None else _vmax)
 				cmap_legend_kws.setdefault("center", self.kwargs.get('center', None))
 				cmap_legend_kws.setdefault("extend", 'both')
 				cmap_legend_kws.setdefault("extendfrac", 0.15)

PyComplexHeatmap/utils.py

@@ -561,7 +561,7 @@ def plot_cmap_legend(
 	cbar_kws.setdefault("fraction", 1)
 	cbar_kws.setdefault("shrink", 1)
 	cbar_kws.setdefault("pad", 0)
-	cbar_kws.setdefault("extend", 'both')
+	cbar_kws.setdefault("extend", 'both') # 'neither', 'both', 'min', 'max'
 	cbar_kws.setdefault("extendfrac", 0.1)
 	vmax = cbar_kws.pop("vmax", 1)
 	vmin = cbar_kws.pop("vmin", 0)
@@ -582,7 +582,26 @@ def plot_cmap_legend(
 	cax.yaxis.set_label_position(label_side)
 	cax.yaxis.set_ticks_position(label_side)
 	cbar = ax.figure.colorbar(m, cax=cax, **cbar_kws)  # use_gridspec=True
-	# cbar.set_ticks([vmin,center,vmax])
+	# Fix white-Line bug in colorbar: Replace the colorbar's QuadMesh body with a single imshow gradient.
+	# matplotlib issue #1188: PDF/SVG viewers render sub-pixel seams between
+	# QuadMesh cells (and between the QuadMesh and the cax border) as thin
+	# white lines. A single imshow image has no internal seams and fills
+	# the cax exactly, so the colorbar body renders cleanly. Outline,
+	# ticks, label and dividers remain vector graphics.
+	cbar.solids.set_visible(False)
+	gradient = np.linspace(vmin, vmax, 1024).reshape(-1, 1)
+	cax.imshow(
+		gradient,
+		aspect="auto",
+		cmap=m.cmap,
+		norm=m.norm,
+		origin="lower",
+		extent=(0, 1, vmin, vmax),
+		interpolation="bilinear",
+		zorder=cbar.solids.get_zorder(),
+	)
+	cax.set_xlim(0, 1)
+	cax.set_ylim(vmin, vmax)
 	# cbar.outline.set_color('white')
 	# cbar.outline.set_linewidth(2)
 	# cbar.dividers.set_color('red')