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mbernstein
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Added ability to control resolution in density_and_location plot
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src/monkeybread/plot/_cell_density.py

Lines changed: 8 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -125,6 +125,8 @@ def location_and_density(
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groups: Union[str, List[str], List[List[str]]],
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groupnames: Optional[Union[str, List[str]]] = None,
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plot_density: Optional[bool] = True,
128+
resolution: Optional[bool] = 10,
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bandwsith: Optional[float] = 75,
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dot_size: Optional[Union[float, List[float]]] = 7,
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na_dot_size: Optional[float] = 1.5,
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title: Optional[str] = None,
@@ -158,6 +160,10 @@ def location_and_density(
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might be ['CD4 T cell', 'CD8 T cell'] that will label the CD4 and CD8 T cells)
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plot_density
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Plot the density plots alongside the embedding plot.
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resolution
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Resolution parameter to pass to :func:`monkeybread.calc.cell_density`
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bandwidth
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Bandwidth parameter to pass to :func:`monkeybread.calc.cell_density`
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dot_size
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The size of dots in the embedding for the cells of intests (specified in `groups`). To plot
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each group with a different dot size, a list of sizes can be provided.
@@ -314,8 +320,8 @@ def location_and_density(
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adata,
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groupby=f'is_{groupname}',
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groups='True',
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resolution=15.0,
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bandwidth=75.
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resolution=resolution,
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bandwidth=bandwidth
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)
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alpha=1.0
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cell_density(

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