update to 1.5.4

Author: DingWB

PyComplexHeatmap/__init__.py

@@ -10,6 +10,6 @@
 from .utils import set_default_style
 
 # __all__=['*']
-__version__ = "1.5.3"
+__version__ = "1.5.4"
 
 _ROOT = os.path.abspath(os.path.dirname(__file__))

PyComplexHeatmap/annotations.py

@@ -59,7 +59,6 @@ class AnnotationBase:
     ----------
     Class AnnotationBase.
     """
-
     def __init__(
         self,
         df=None,
@@ -225,12 +224,8 @@ def _calculate_cmap(self):
     def _type_specific_params(self):
         pass
 
-    def reorder(
-        self, idx
-    ):  # Before plotting, df needs to be reordered according to the new clustered order.
-        """
-        idx: list
-        """
+    def reorder(self, idx):
+        # Before plotting, df needs to be reordered according to the new clustered order.
         # n_overlap = len(set(self.df.index.tolist()) & set(idx))
         # if n_overlap == 0:
         #     raise ValueError("The input idx is not consistent with the df.index")
@@ -243,7 +238,7 @@ def reorder(
     def get_label_width(self):
         return self.ax.yaxis.label.get_window_extent(
             renderer=self.ax.figure.canvas.get_renderer()
-        ).width  #
+        ).width
 
     def get_ticklabel_width(self):
         yticklabels = self.ax.yaxis.get_ticklabels()
@@ -266,9 +261,8 @@ def get_max_label_width(self):
 # =============================================================================
 class anno_simple(AnnotationBase):
     """
-    Annotate simple annotation, categorical or continuous variables.
+        Annotate simple annotation, categorical or continuous variables.
     """
-
     def __init__(
         self,
         df=None,
@@ -456,7 +450,6 @@ class anno_label(AnnotationBase):
     Class AnnotationBase.
 
     """
-
     def __init__(
         self,
         df=None,
@@ -1175,7 +1168,6 @@ class HeatmapAnnotation:
     Class HeatmapAnnotation.
 
     """
-
     def __init__(
         self,
         df=None,

PyComplexHeatmap/clustermap.py

@@ -542,9 +542,7 @@ def plot_heatmap(
 ):
     """
     Plot heatmap.
-        heatmap(self.data2d.loc[rows, cols], ax=ax1,cmap=self.cmap,
-                        mask=self.mask.loc[rows, cols], rasterized=self.rasterized,
-                        xticklabels='auto', yticklabels='auto', annot=annot1, **self.kwargs)
+
     Parameters
     ----------
     data: dataframe
@@ -709,7 +707,6 @@ class DendrogramPlotter(object):
     def __init__(
         self, data, linkage, metric, method, axis, label, rotate, dendrogram_kws=None
     ):
-        """Plot a dendrogram of the relationships between the columns of data"""
         self.axis = axis
         if (
             self.axis == 1
@@ -949,6 +946,10 @@ class ClusterMapPlotter:
         kws passed to hierarchy.dendrogram.
     tree_kws :dict
         kws passed to DendrogramPlotter.plot()
+    row_split_order: list
+        a list to specify the order of row_split.
+    col_split_order: list
+        a list to specify the order of col_split.
     row_split_gap :float
         default are 0.5 and 0.2 mm for row and col.
     col_split_gap :float
@@ -961,14 +962,14 @@ class ClusterMapPlotter:
         True or False, whether to plot heatmap legend, determined by cmap.
     legend_kws :dict
         kws passed to plot legend. If one want to change the outline color and linewidth of cbar:
-        ```
+
         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)
-        ```
+
     plot :bool
         whether to plot or not.
     plot_legend :bool
@@ -1006,7 +1007,6 @@ class ClusterMapPlotter:
     -------
     Class ClusterMapPlotter.
     """
-
     def __init__(
         self,
         data,

PyComplexHeatmap/dotHeatmap.py

@@ -297,7 +297,6 @@ class DotClustermapPlotter(ClusterMapPlotter):
     -------
     DotClustermapPlotter.
     """
-
     def __init__(
         self,
         data=None,

PyComplexHeatmap/oncoPrint.py

@@ -185,7 +185,6 @@ class oncoPrintPlotter(ClusterMapPlotter):
     -------
     oncoPrintPlotter.
     """
-
     def __init__(
         self,
         data=None,

PyComplexHeatmap/utils.py

@@ -45,11 +45,18 @@ def get_colormap(cmap):
 
 def _check_mask(data, mask):
     """
-
-    Ensure that data and mask are compatible and add missing values and infinite values.
+        Ensure that data and mask are compatible and add missing values and infinite values.
     Values will be plotted for cells where ``mask`` is ``False``.
-    ``data`` is expected to be a DataFrame; ``mask`` can be an array or
-    a DataFrame.
+     ``data`` is expected to be a DataFrame; ``mask`` can be an array or a DataFrame.
+
+    Parameters
+    ----------
+    data
+    mask
+
+    Returns
+    -------
+
     """
     if mask is None:
         mask = np.zeros(data.shape, bool)
@@ -94,7 +101,10 @@ def _calculate_luminance(color):
 def define_cmap(
     plot_data, vmin=None, vmax=None, cmap=None, center=None, robust=True, na_col="white"
 ):
-    """Use some heuristics to set good defaults for colorbar and range."""
+    """
+    Use some heuristics to set good defaults for colorbar and range.
+
+    """
     # plot_data is a np.ma.array instance
     # plot_data=np.ma.masked_where(np.asarray(plot_data), plot_data)
     # calc_data = plot_data.astype(float).filled(np.nan)
@@ -240,7 +250,10 @@ def axis_ticklabels_overlap(labels):
 # =============================================================================
 # =============================================================================
 def _skip_ticks(labels, tickevery):
-    """Return ticks and labels at evenly spaced intervals."""
+    """
+    Return ticks and labels at evenly spaced intervals.
+
+    """
     n = len(labels)
     if tickevery == 0:
         ticks, labels = [], []
@@ -255,7 +268,10 @@ def _skip_ticks(labels, tickevery):
 
 # =============================================================================
 def _auto_ticks(ax, labels, axis):
-    """Determine ticks and ticklabels that minimize overlap."""
+    """
+    Determine ticks and ticklabels that minimize overlap.
+
+    """
     transform = ax.figure.dpi_scale_trans.inverted()
     bbox = ax.get_window_extent().transformed(transform)
     size = [bbox.width, bbox.height][axis]