add parameter cbar_height & update docs

Author: DingWB

PyComplexHeatmap/annotations.py

@@ -50,6 +50,7 @@ class AnnotationBase:
 		`legend_kws={'color_text':False}`, then, black would be the default color for the text.
 		If the user want to use a custom color instead of black (such as blue), please set
 		legend_kws={'color_text':False,'labelcolor':'blue'}.
+		An extra parameter `cbar_height` could be passed in legend_kws to control the height of the colorbar for heatmap, default is 15 [mm].
 	ylim: tuple
 		y axis limits for the annotation when axis=1, x axis limits when axis=0.
 	label: str
@@ -453,12 +454,10 @@ class anno_label(AnnotationBase):
 		passed to plt.annotate, including annotation_clip, arrowprops and matplotlib.text.Text,
 		more information about arrowprops could be found in
 		matplotlib.patches.FancyArrowPatch. For example, to remove arrow, just set
-		arrowprops = dict(visible=False). See: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.annotate.html for more information.
-		arrowprops:
-			arrowstyle:
-				https://matplotlib.org/stable/gallery/text_labels_and_annotations/fancyarrow_demo.html
-			connectionstyle:
-				https://matplotlib.org/stable/gallery/userdemo/connectionstyle_demo.html
+		arrowprops = dict(visible=False). See https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.annotate.html for more information.
+
+		- arrowprops.arrowstyle: https://matplotlib.org/stable/gallery/text_labels_and_annotations/fancyarrow_demo.html
+		- arrowprops.connectionstyle: https://matplotlib.org/stable/gallery/userdemo/connectionstyle_demo.html
 
 	Returns
 	----------
@@ -2038,7 +2037,7 @@ def collect_legends(self):
 					[
 						annotation.cmap,
 						annotation.label,
-						legend_kws, 4, "cmap"]
+						legend_kws, legend_kws.pop('cbar_height',15), "cmap"]
 				)
 		self.get_legend_list() #self.legend_list will be created
 

PyComplexHeatmap/clustermap.py

@@ -936,14 +936,16 @@ def get_coords(self,ax,gap_pixel=None,root_x=None):
 	def plot(self, ax, gap_pixel=None, root_x=None,tree_kws=None,
 			 bezier=False,dotsize=1,root_dot=True,axis=1,label=False,
 			 orientation=None,invert=True):
-		"""Plots a dendrogram of the similarities between data on the axes
+		"""Plots a dendrogram of the similarities between data on the axes.
+
 		Parameters
 		----------
 		ax : matplotlib.axes.Axes
 			Axes object upon which the dendrogram is plotted
 		axis : int
 			0 for rows (default) and 1 for columns.
 		label : bool
+			Whether to show labels on the dendrogram.
 		rotate : bool
 			If axis==0 and one would like to plot row dendrogram, rotate
 			should be True
@@ -1144,16 +1146,19 @@ class ClusterMapPlotter:
 	legend_kws :dict
 		vmax, vmin and other kws passed to plot legend, such as
 		use_gridspec, location, orientation, fraction, shrink, aspect, pad, anchor, panchor,
-		extend, extendfrac, extendrect, ticks, format, drawedges, label, doundaries, values, spacing:
-		```
-		cm=ClusterMapPlotter(...)
-		for cbar in cm.cbars:
-		if isinstance(cbar,matplotlib.colorbar.Colorbar):
-			cbar.outline.set_color('white')
-			cbar.outline.set_linewidth(2)
-			cbar.dividers.set_color('red')
-			cbar.dividers.set_linewidth(2)
-		```
+		extend, extendfrac, extendrect, ticks, format, drawedges, label, doundaries, values, spacing.
+		Default extend is set to 'both' (change to neither to turn off) and default extendfrac is set to 0.1
+		An extra parameter ``cbar_height`` could be passed in legend_kws to control the height of the colorbar for heatmap, default is 20 [mm].
+		Example::
+
+			cm=ClusterMapPlotter(...)
+			for cbar in cm.cbars:
+				if isinstance(cbar,matplotlib.colorbar.Colorbar):
+					cbar.outline.set_color('white')
+					cbar.outline.set_linewidth(2)
+					cbar.dividers.set_color('red')
+					cbar.dividers.set_linewidth(2)
+
 		In addition to vmax,vmin, other parameters will be passed to https://matplotlib.org/stable/api/_as_gen/matplotlib.figure.Figure.colorbar.html#matplotlib.figure.Figure.colorbar
 
 	plot :bool
@@ -1198,14 +1203,12 @@ class ClusterMapPlotter:
 		alpha,color,fontfamily,fontname,fontproperties,fontsize,fontstyle,
 		fontweight,label,rasterized,rotation,rotation_mode(default,anchor),visible,
 		zorder,verticalalignment,horizontalalignment.
-		See ax.xaxis.label.properties(), for example:
-		```
-		cm=ClusterMapPlotter(***), print(cm.ax.xaxis.label.properties())
-		```
-		or
-		```
-		matplotlib.axis.XAxis.label.properties() for detail.
-		```
+		See ax.xaxis.label.properties(), for example::
+
+			cm=ClusterMapPlotter(...)
+			print(cm.ax.xaxis.label.properties())
+
+		or ``matplotlib.axis.XAxis.label.properties()`` for detail.
 	ylabel_kws: dict
 		sams as xlabel_kws
 	xlabel_side: str
@@ -1216,10 +1219,11 @@ class ClusterMapPlotter:
 		alpha,clip_box, clip_on,edgecolor,facecolor,fill,height,in_layout,label,
 		linestyle, linewidth,rasterized,visible,width.
 		See ax.xaxis.label.get_bbox_patch().properties() for more information.
-		For example:
-		```
-		cm=ClusterMapPlotter(***), print(cm.ax.xaxis.label.get_bbox_patch().properties())
-		```
+		For example::
+
+			cm=ClusterMapPlotter(...)
+			print(cm.ax.xaxis.label.get_bbox_patch().properties())
+
 	ylabel_bbox_kws: dict
 		same as xlabel_bbox_kws
 	rasterized :bool
@@ -2307,7 +2311,10 @@ 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_dict[self.label]=tuple([self.cmap, self.label, self.legend_kws, 4, "cmap"])
+			self.legend_kws.setdefault("extend", 'both')
+			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"])
 			if len(self.yticklabels) > 0 and self.row_names_side == "right":
 				max_yticklabel_w = max(
 					[label.get_window_extent().width for label in self.yticklabels]

PyComplexHeatmap/dotHeatmap.py

@@ -599,22 +599,28 @@ def collect_legends(self):
 					cmap_legend_kws.setdefault("vmin", self.kwargs.get('vmin'))  # round(vmin, 2))
 					cmap_legend_kws.setdefault("vmax", self.kwargs.get('vmax'))  # round(vmax, 2))
 					cmap_legend_kws.setdefault("center", self.kwargs.get('center', None))
+					cmap_legend_kws.setdefault("extend", 'both')
+					cmap_legend_kws.setdefault("extendfrac", 0.15)
+					cbar_height=cmap_legend_kws.pop('cbar_height',20)
 					for key in self.cmap:
-						self.legend_dict[f"{key} (cmap)"]=tuple([self.cmap[key], key, cmap_legend_kws, 4, "cmap"])
+						self.legend_dict[f"{key} (cmap)"]=tuple([self.cmap[key], key, cmap_legend_kws, cbar_height, "cmap"])
 			else: # hue is None
 				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))
 				cmap_legend_kws.setdefault("center", self.kwargs.get('center', None))
+				cmap_legend_kws.setdefault("extend", 'both')
+				cmap_legend_kws.setdefault("extendfrac", 0.15)
+				cbar_height=cmap_legend_kws.pop('cbar_height',20)
 				if (
 					not cmap is None
 					and type(cmap) == str
 					and not c is None
 					and type(c) != str
 				):
-					self.legend_dict[f"{self.value} (cmap)"]=tuple([cmap, self.value, cmap_legend_kws, 4, "cmap"])
+					self.legend_dict[f"{self.value} (cmap)"]=tuple([cmap, self.value, cmap_legend_kws, cbar_height, "cmap"])
 			# dot size legend:
 			if type(self.s) == str:
 				# s=self.kwargs.get('s',None)

PyComplexHeatmap/utils.py

@@ -210,7 +210,7 @@ def despine(fig=None, ax=None, top=True, right=True, left=False, bottom=False):
 
 
 # =============================================================================
-def _draw_figure(fig):
+def _draw_figure_deprecated(fig):
 	"""
 	Force draw of a matplotlib figure, accounting for back-compat.
 
@@ -223,6 +223,17 @@ def _draw_figure(fig):
 		except AttributeError:
 			pass
 
+def _draw_figure(fig):
+	"""
+	Force draw of a matplotlib figure, accounting for back-compat.
+	fig.canvas.draw() re-renders the entire figure (every axis, every artist), which is very expensive for complex heatmaps. get_renderer() just returns the renderer object so you can measure sizes without triggering a full draw.
+
+	"""
+	try:
+		renderer = fig.canvas.get_renderer()
+	except AttributeError:
+		fig.canvas.draw()
+		renderer = fig.canvas.get_renderer()
 
 # =============================================================================
 def axis_ticklabels_overlap(labels):
@@ -364,10 +375,15 @@ def cluster_labels(labels=None, xticks=None, majority=True):
 	"""
 	clusters_x = collections.defaultdict(list)
 	clusters_labels = {}
-	scanned_labels = ""
+	_sentinel = object()
+	scanned_labels = _sentinel
 	i = 0
 	for label, x in zip(labels, xticks):
-		if label != scanned_labels:
+		is_nan = pd.isna(label)
+		prev_is_nan = scanned_labels is not _sentinel and pd.isna(scanned_labels)
+		if is_nan and prev_is_nan:
+			pass  # consecutive NaNs belong to the same cluster
+		elif is_nan or label != scanned_labels:
 			scanned_labels = label
 			i += 1
 			clusters_labels[i] = scanned_labels
@@ -376,18 +392,20 @@ def cluster_labels(labels=None, xticks=None, majority=True):
 		cluster_size = collections.defaultdict(int)
 		largest_cluster = {}
 		for i in clusters_labels:
-			if len(clusters_x[i]) > cluster_size[clusters_labels[i]]:
-				cluster_size[clusters_labels[i]] = len(clusters_x[i])
-				largest_cluster[clusters_labels[i]] = i
+			lbl = clusters_labels[i]
+			key = lbl if not pd.isna(lbl) else "__nan__"
+			if len(clusters_x[i]) > cluster_size[key]:
+				cluster_size[key] = len(clusters_x[i])
+				largest_cluster[key] = i
 		labels = [
 			clusters_labels[i]
 			for i in clusters_x
-			if i == largest_cluster[clusters_labels[i]]
+			if i == largest_cluster[clusters_labels[i] if not pd.isna(clusters_labels[i]) else "__nan__"]
 		]
 		x = [
 			np.mean(clusters_x[i])
 			for i in clusters_x
-			if i == largest_cluster[clusters_labels[i]]
+			if i == largest_cluster[clusters_labels[i] if not pd.isna(clusters_labels[i]) else "__nan__"]
 		]
 		return labels, x
 
@@ -543,8 +561,8 @@ 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("extendfrac", 0.1)
+	cbar_kws.setdefault("extend", 'both')
+	cbar_kws.setdefault("extendfrac", 0.1)
 	vmax = cbar_kws.pop("vmax", 1)
 	vmin = cbar_kws.pop("vmin", 0)
 	# print(vmin,vmax,'vmax,vmin')
@@ -765,14 +783,11 @@ def plot_legend_list(
 		)  # labelpad unit is points
 		left = ax.get_position().x1 + pad
 	if legend_width is None:
-		# try:
 		legend_width = (
 			cal_legend_width(legend_list) + 3
 		)  # base width for color rectangle is set to 3 mm
 		if verbose > 0:
 			print(f"Estimated legend width: {legend_width} mm")
-		# except:
-		# 	legend_width=15
 	legend_width = (
 		legend_width * mm2inch * ax.figure.dpi / ax.figure.get_window_extent().width
 	)  # mm to px to fraction
@@ -803,14 +818,14 @@ def plot_legend_list(
 	h_gap=h_gap * mm2inch * ax.figure.dpi # pixels
 	i = 0
 	while i <= len(legend_list) - 1:
-		obj, title, legend_kws, n, lgd_t = legend_list[i]
+		obj, title, legend_kws, lgd_h, lgd_t = legend_list[i]
 		ax1 = legend_axes[-1]  # ax for the legend on the right
 		ax1.set_axis_off()
 		color_text = legend_kws.pop("color_text", True)
 		if lgd_t == "cmap":  # type(obj)==str: # a cmap, plot colorbar
 			f = (
-				15 * mm2inch * ax.figure.dpi / ax.figure.get_window_extent().height
-			)  # 15 mm
+				lgd_h * mm2inch * ax.figure.dpi / ax.figure.get_window_extent().height
+			)  # 15 mm in default for colorbar height, f is a fraction of legend height
 			if y - f < 0:  # add a new column of axes to plot legends
 				offset = (
 					lgd_col_max_width + h_gap + ax.yaxis.labelpad * ax.figure.dpi / 72
@@ -861,7 +876,7 @@ def plot_legend_list(
 			# print(obj, title, legend_kws)
 			legend_kws["bbox_to_anchor"] = (
 				leg_pos.x0,
-				y,
+				y, # y is the bottom position of the first legend (from top to the bottom)
 			)  # lower left position of the box.
 			# x, y, width, height #kws['bbox_transform'] = ax.figure.transFigure
 			# ax1.scatter(leg_pos.x0,y,s=6,color='red',zorder=20,transform=ax1.figure.transFigure)

docs/build/doctrees/PyComplexHeatmap.annotations.doctree

@@ -1540,21 +1540,13 @@
     "plt.savefig(\"oncoPrint.horizontal.pdf\",bbox_inches='tight')\n",
     "plt.show()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "5411e7cd-8b50-4d7d-bbd4-df4b4b0b9288",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "m3c",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "m3c"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1566,7 +1558,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.18"
+   "version": "3.8.19"
   }
  },
  "nbformat": 4,