Update pymaf.MafFrame.plot_mutated_matched:

* Add new optional argument ``count`` to :meth:`pymaf.MafFrame.plot_mutated_matched` method.
sbslee · Aug 10, 2022 · c4b6a42 · c4b6a42
1 parent dd92ed8
commit c4b6a42
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -9,6 +9,7 @@ Changelog
 * Add new method :meth:`pyvcf.VcfFrame.filter_gsa`.
 * Add new method :meth:`pyvcf.VcfFrame.duplicated`.
 * Add new optional argument ``to_csv`` to :meth:`pymaf.MafFrame.plot_regplot_tmb` method.
+* Add new optional argument ``count`` to :meth:`pymaf.MafFrame.plot_mutated_matched` method.
 
 0.35.0 (2022-07-12)
 -------------------

diff --git a/fuc/api/pymaf.py b/fuc/api/pymaf.py
@@ -1811,8 +1811,8 @@ def plot_mutated(
  return ax
 
  def plot_mutated_matched(
- self, af, patient_col, group_col, group_order, ax=None, figsize=None,
- **kwargs
+ self, af, patient_col, group_col, group_order, count=10, ax=None,
+ figsize=None, **kwargs
  ):
  """
  Create a bar plot visualizing the mutation prevalence of top
@@ -1828,6 +1828,8 @@ def plot_mutated_matched(
  AnnFrame column containing sample group information.
  group_order : list
  List of sample group names.
+ count : int, defualt: 10
+ Number of top mutated genes to display.
  ax : matplotlib.axes.Axes, optional
  Pre-existing axes for the plot. Otherwise, crete a new one.
  figsize : tuple, optional
@@ -1841,7 +1843,7 @@ def plot_mutated_matched(
  matplotlib.axes.Axes
  The matplotlib axes containing the plot.
  """
- df = self.matrix_waterfall_matched(af, patient_col, group_col, group_order)
+ df = self.matrix_waterfall_matched(af, patient_col, group_col, group_order, count=count)
  df = df.applymap(lambda x: 0 if x == 'None' else 1)
  s = df.sum(axis=1) / len(df.columns) * 100
  s.name = 'Count'