scimap.pl.pie

Short description

The sm.pl.pie function allows users to visualize proportions of cell-types or any categorical data in the form of a pie plot.

Parameters

adata : AnnData object

phenotype : string, optional (The default is phenotype)
Column contaning the cell-type inforamtion or any categorical data to be displayed in the form of a pie plot.

group_by : string, optional (The default is imageid)
Column that contains inforamtion on data groupings which leads to generation of pie plot for each group (e.g. image-id). If None is passed, the entire data is considered as a single group.

ncols : int, optional (The default is None)
In case group_by is used, a grid of plots are returned. This paramenter controls the number of columns in that grid.

subset_phenotype : list, optional (The default is None)
User can subset a list of categories within phenotype before plotting.

subset_groupby : list, optional (The default is None)
User can subset a list of categories within group_by before plotting.

label : list, optional (The default is auto)
A list of strings providing the labels for each wedge.

title : string, optional (The default is auto)
If None, the title of the pieplot is not plotted.

colors : list, optional (The default is None)
A sequence of colors through which the pie chart will cycle. If None, will use the colors in the currently active cycle.

autopct : None or str or callable, optional (The default is '%1.1f%%')
If not None, is a string or function used to label the wedges with their numeric value. The label will be placed inside the wedge. If it is a format string, the label will be fmt % pct. If it is a function, it will be called.

wedgeprops : dict, optional (The default is {'linewidth': 0})
Dict of arguments passed to the wedge objects making the pie. For example, you can pass in wedgeprops = {'linewidth': 3} to set the width of the wedge border lines equal to 3. For more details, look at the doc/arguments of the wedge object.

return_data : bool, optional (The default is False)
When True, return the data used for plotting.

**kwargs : Keyword arguments to pass on to matplotlib.pyplot.pie

Returns

If return_data is set to True, the function returns a dataframe of the data used for the plotting.

Example

# pie plot showing stromal tumor content among the different samples
sm.pl.pie (adata, phenotype='Tumor_Stroma', group_by='imageid', 
           autopct='%1.1f%%',
           textprops={'fontsize': 8, 'color': '#1d3557', 'fontweight': 'bold'},
           ncols=5, label=None, title=None, 
           colors=['#a8dadc','#e63946'], 
           wedgeprops = {'linewidth': 0.8})