update anno_img:

(1). support missing value (2). automatically resize to the minimal sizes (3) fix bug about invert and order of images
DingWB · Apr 19, 2024 · 018a9d0 · 018a9d0
1 parent 8c38982
commit 018a9d0
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Showing 56 changed files with 813 additions and 811 deletions.
diff --git a/PyComplexHeatmap/annotations.py b/PyComplexHeatmap/annotations.py
@@ -223,10 +223,10 @@ def _calculate_cmap(self):
 
 	def _type_specific_params(self):
 		if self.ylim is None:
-			Max = np.nanmax(self.df.values)
-			Min = np.nanmin(self.df.values)
+			Max = np.nanmax(self.df.sum(axis=1).values)
+			Min = np.nanmin(self.df.sum(axis=1).values)
 			gap = Max - Min
-			self.ylim = [Min - 0.02 * gap, Max + 0.02 * gap]
+			self.ylim = [Min - 0.05 * gap, Max + 0.05 * gap]
 
 	def reorder(self, idx):
 		# Before plotting, df needs to be reordered according to the new clustered order.
@@ -557,6 +557,7 @@ def _calculate_cmap(self):
 
 	def _type_specific_params(self):
 		pass
+
 	def plot(self, ax=None, axis=1):  # add self.gs,self.fig,self.ax,self.axes
 		self.axis = axis
 		if self.orientation is None:
@@ -871,10 +872,10 @@ def _calculate_cmap(self):
 
 	def _type_specific_params(self):
 		if self.ylim is None:
-			Max = np.nanmax(self.df.values)
-			Min = np.nanmin(self.df.values)
+			Max = np.nanmax(self.df.sum(axis=1).values)
+			Min = np.nanmin(self.df.sum(axis=1).values)
 			gap = Max - Min
-			self.ylim = [Min - 0.02 * gap, Max + 0.02 * gap]
+			self.ylim = [Min - 0.05 * gap, Max + 0.05 * gap]
 		if self.ncols > 1:
 			self.stacked = True
 		else:
@@ -996,11 +997,11 @@ def _calculate_cmap(self):
 		self.set_legend(False)
 
 	def _type_specific_params(self):
-		Max = np.nanmax(self.df.values)
-		Min = np.nanmin(self.df.values)
+		Max = np.nanmax(self.df.sum(axis=1).values)
+		Min = np.nanmin(self.df.sum(axis=1).values)
 		self.gap = Max - Min
 		if self.ylim is None:
-			self.ylim = [Min - 0.02 * self.gap, Max + 0.02 * self.gap]
+			self.ylim = [Min - 0.05 * self.gap, Max + 0.05 * self.gap]
 
 	def plot(self, ax=None, axis=1):  # add self.gs,self.fig,self.ax,self.axes
 		if ax is None:

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diff --git a/docs/build/html/_modules/PyComplexHeatmap/annotations.html b/docs/build/html/_modules/PyComplexHeatmap/annotations.html
@@ -571,10 +571,10 @@ <h1>Source code for PyComplexHeatmap.annotations</h1><div class="highlight"><pre
 
 	<span class="k">def</span> <span class="nf">_type_specific_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 		<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ylim</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-			<span class="n">Max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmax</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
-			<span class="n">Min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmin</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
+			<span class="n">Max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmax</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
+			<span class="n">Min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmin</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
 			<span class="n">gap</span> <span class="o">=</span> <span class="n">Max</span> <span class="o">-</span> <span class="n">Min</span>
-			<span class="bp">self</span><span class="o">.</span><span class="n">ylim</span> <span class="o">=</span> <span class="p">[</span><span class="n">Min</span> <span class="o">-</span> <span class="mf">0.02</span> <span class="o">*</span> <span class="n">gap</span><span class="p">,</span> <span class="n">Max</span> <span class="o">+</span> <span class="mf">0.02</span> <span class="o">*</span> <span class="n">gap</span><span class="p">]</span>
+			<span class="bp">self</span><span class="o">.</span><span class="n">ylim</span> <span class="o">=</span> <span class="p">[</span><span class="n">Min</span> <span class="o">-</span> <span class="mf">0.05</span> <span class="o">*</span> <span class="n">gap</span><span class="p">,</span> <span class="n">Max</span> <span class="o">+</span> <span class="mf">0.05</span> <span class="o">*</span> <span class="n">gap</span><span class="p">]</span>
 
 <div class="viewcode-block" id="AnnotationBase.reorder"><a class="viewcode-back" href="../../PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.AnnotationBase.reorder">[docs]</a>	<span class="k">def</span> <span class="nf">reorder</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">idx</span><span class="p">):</span>
 		<span class="c1"># Before plotting, df needs to be reordered according to the new clustered order.</span>
@@ -905,6 +905,7 @@ <h1>Source code for PyComplexHeatmap.annotations</h1><div class="highlight"><pre
 
 	<span class="k">def</span> <span class="nf">_type_specific_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 		<span class="k">pass</span>
+
 <div class="viewcode-block" id="anno_label.plot"><a class="viewcode-back" href="../../PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_label.plot">[docs]</a>	<span class="k">def</span> <span class="nf">plot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ax</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>  <span class="c1"># add self.gs,self.fig,self.ax,self.axes</span>
 		<span class="bp">self</span><span class="o">.</span><span class="n">axis</span> <span class="o">=</span> <span class="n">axis</span>
 		<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">orientation</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -1219,10 +1220,10 @@ <h1>Source code for PyComplexHeatmap.annotations</h1><div class="highlight"><pre
 
 	<span class="k">def</span> <span class="nf">_type_specific_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 		<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ylim</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-			<span class="n">Max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmax</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
-			<span class="n">Min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmin</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
+			<span class="n">Max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmax</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
+			<span class="n">Min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmin</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
 			<span class="n">gap</span> <span class="o">=</span> <span class="n">Max</span> <span class="o">-</span> <span class="n">Min</span>
-			<span class="bp">self</span><span class="o">.</span><span class="n">ylim</span> <span class="o">=</span> <span class="p">[</span><span class="n">Min</span> <span class="o">-</span> <span class="mf">0.02</span> <span class="o">*</span> <span class="n">gap</span><span class="p">,</span> <span class="n">Max</span> <span class="o">+</span> <span class="mf">0.02</span> <span class="o">*</span> <span class="n">gap</span><span class="p">]</span>
+			<span class="bp">self</span><span class="o">.</span><span class="n">ylim</span> <span class="o">=</span> <span class="p">[</span><span class="n">Min</span> <span class="o">-</span> <span class="mf">0.05</span> <span class="o">*</span> <span class="n">gap</span><span class="p">,</span> <span class="n">Max</span> <span class="o">+</span> <span class="mf">0.05</span> <span class="o">*</span> <span class="n">gap</span><span class="p">]</span>
 		<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ncols</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
 			<span class="bp">self</span><span class="o">.</span><span class="n">stacked</span> <span class="o">=</span> <span class="kc">True</span>
 		<span class="k">else</span><span class="p">:</span>
@@ -1344,11 +1345,11 @@ <h1>Source code for PyComplexHeatmap.annotations</h1><div class="highlight"><pre
 		<span class="bp">self</span><span class="o">.</span><span class="n">set_legend</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
 
 	<span class="k">def</span> <span class="nf">_type_specific_params</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-		<span class="n">Max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmax</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
-		<span class="n">Min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmin</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
+		<span class="n">Max</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmax</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
+		<span class="n">Min</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nanmin</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">)</span>
 		<span class="bp">self</span><span class="o">.</span><span class="n">gap</span> <span class="o">=</span> <span class="n">Max</span> <span class="o">-</span> <span class="n">Min</span>
 		<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">ylim</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-			<span class="bp">self</span><span class="o">.</span><span class="n">ylim</span> <span class="o">=</span> <span class="p">[</span><span class="n">Min</span> <span class="o">-</span> <span class="mf">0.02</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">gap</span><span class="p">,</span> <span class="n">Max</span> <span class="o">+</span> <span class="mf">0.02</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">gap</span><span class="p">]</span>
+			<span class="bp">self</span><span class="o">.</span><span class="n">ylim</span> <span class="o">=</span> <span class="p">[</span><span class="n">Min</span> <span class="o">-</span> <span class="mf">0.05</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">gap</span><span class="p">,</span> <span class="n">Max</span> <span class="o">+</span> <span class="mf">0.05</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">gap</span><span class="p">]</span>
 
 <div class="viewcode-block" id="anno_scatterplot.plot"><a class="viewcode-back" href="../../PyComplexHeatmap.annotations.html#PyComplexHeatmap.annotations.anno_scatterplot.plot">[docs]</a>	<span class="k">def</span> <span class="nf">plot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ax</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>  <span class="c1"># add self.gs,self.fig,self.ax,self.axes</span>
 		<span class="k">if</span> <span class="n">ax</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>

diff --git a/docs/build/html/_sources/notebooks/advanced_usage.ipynb.txt b/docs/build/html/_sources/notebooks/advanced_usage.ipynb.txt