update default vmax,vmin for legend_kws and add default pdf.fonttype

Author: Wubin Ding

PyComplexHeatmap/__init__.py

@@ -7,7 +7,7 @@
 from .dotHeatmap import *
 from .colors import *
 from .tools import *
-# from .example import *
+from .utils import set_default_style
 
 #__all__=['*']
 __version__='1.4.2'

PyComplexHeatmap/annotations.py

@@ -238,6 +238,11 @@ def __init__(self, df=None, cmap='auto', colors=None, add_text=False,
         self.text_kws = text_kws if not text_kws is None else {}
         self.plot_kws = plot_kws
         # print(self.plot_kws)
+        legend_kws = legend_kws if not legend_kws is None else {}
+        if 'vmax' in plot_kws:
+            legend_kws.setdefault('vmax', plot_kws.get('vmax'))
+        if 'vmin' in plot_kws:
+            legend_kws.setdefault('vmin', plot_kws.get('vmin'))
         super().__init__(df=df, cmap=cmap, colors=colors,
                          height=height, legend=legend, legend_kws=legend_kws, **plot_kws)
 

PyComplexHeatmap/clustermap.py

@@ -1003,11 +1003,13 @@ def _reorder_rows(self):
                 self.row_split = self.row_split.to_frame(name=self.row_split.name)
             cols = self.row_split.columns.tolist()
             row_clusters = self.row_split.groupby(cols).apply(lambda x: x.index.tolist())
-            if self.row_split_order is None:
+            if len(cols)==1 and self.row_split_order is None:
                 # calculate row_split_order using the mean across all samples in this group of
                 # values of mean values across all samples
                 self.row_split_order = row_clusters.apply(lambda x: self.data2d.loc[x].mean(axis=1).mean())\
                     .sort_values(ascending=False).index.tolist()
+            else:
+                self.row_split_order=row_clusters.sort_index().index.tolist()
             self.row_clusters = row_clusters.loc[self.row_split_order].to_dict()
         elif not self.row_cluster:
             self.row_order = [self.data2d.index.tolist()]
@@ -1050,11 +1052,13 @@ def _reorder_cols(self):
                 self.col_split = self.col_split.to_frame(name=self.col_split.name)
             cols = self.col_split.columns.tolist()
             col_clusters = self.col_split.groupby(cols).apply(lambda x: x.index.tolist())
-            if self.col_split_order is None:
+            if len(cols)==1 and self.col_split_order is None:
                 # calculate col_split_order using the mean across all samples in this group of
                 # values of mean values across all samples
                 self.col_split_order = col_clusters.apply(lambda x: self.data2d.loc[:,x].mean().mean())\
                     .sort_values(ascending=False).index.tolist()
+            else:
+                self.col_split_order=col_clusters.sort_index().index.tolist()
             self.col_clusters = col_clusters.loc[self.col_split_order].to_dict()
         elif not self.col_cluster:
             self.col_order = [self.data2d.columns.tolist()]

PyComplexHeatmap/colors.py

@@ -5,8 +5,6 @@
 from matplotlib.colors import LinearSegmentedColormap,ListedColormap,CSS4_COLORS
 import random
 from .utils import _calculate_luminance
-plt.rcParams['figure.dpi'] = 100
-plt.rcParams['savefig.dpi']=300
 
 def define_cmap():
     all_cmaps=matplotlib.pyplot.colormaps()

PyComplexHeatmap/utils.py

@@ -11,6 +11,26 @@
 import matplotlib.patches as mpatches
 mm2inch=1/25.4
 # =============================================================================
+def set_default_style():
+    from matplotlib import rcParams
+    D={
+        'font.family':['sans serif'], #'serif',
+        # 'mathtext.fontset':'dejavuserif',
+        'font.sans-serif':['Arial'],
+        'pdf.fonttype':42,
+
+        # Remove legend frame
+        'legend.frameon': True,
+
+        # Savefig
+        'figure.dpi': 100,
+        'savefig.bbox': 'tight',
+        'savefig.dpi':300,
+        'savefig.pad_inches': 0.05
+    }
+    
+    rcParams.update(D)
+# =============================================================================
 def _check_mask(data, mask):
     """
 
@@ -373,6 +393,7 @@ def plot_cmap_legend(cax=None,ax=None,cmap='turbo',label=None,kws=None,label_sid
     """
     label='' if label is None else label
     cbar_kws={} if kws is None else kws.copy()
+    cbar_kws.setdefault('label',label)
     # cbar_kws.setdefault("aspect",3)
     cbar_kws.setdefault("orientation","vertical")
     # cbar_kws.setdefault("use_gridspec", True)
@@ -390,7 +411,7 @@ def plot_cmap_legend(cax=None,ax=None,cmap='turbo',label=None,kws=None,label_sid
         cmap=cmap)
     cax.yaxis.set_label_position(label_side)
     cax.yaxis.set_ticks_position(label_side)
-    cbar=ax.figure.colorbar(m,cax=cax,label=label,**cbar_kws) #use_gridspec=True
+    cbar=ax.figure.colorbar(m,cax=cax,**cbar_kws) #use_gridspec=True
     # cbar.outline.set_color('white')
     # cbar.outline.set_linewidth(2)
     # cbar.dividers.set_color('red')
@@ -633,4 +654,6 @@ def plot_legend_list(legend_list=None,ax=None,space=0,legend_side='right',
     else:
         boundry = ax1.get_position().y0 - max_width / ax.figure.get_window_extent().width
     return legend_axes,cbars,boundry
-# =============================================================================
+# =============================================================================
+
+set_default_style()