scimap.pl.foldchange

Short description

The sm.pl.foldchange function allows users to visualize foldchanges in celltypes between samples/ROI's. Run sm.tl.foldchange first to compute the foldchange.

The function incorportates two methods.
a) A Heatmap plot - Use method = 'heatmap'
b) Parallel Coordinates plot : Use method = 'parallel_coordinates'

Parameters

adata : AnnData object

label : string, optional (The default is foldchange)
label used when running sm.tl.foldchange.

p_val : float, optional (The default is 0.05)
p_val cut-off above which is considered not-significant. The cells containing non-significant changes will be highlighted in the heatmap.

method : string, optional (The default is heatmap)
Two methods are available for plotting the foldchanges
a) Heatmap: Use heatmap
b) parallel coordinates plot : Use parallel_coordinates

nonsig_color : string, optional (The default is grey)
Color used to highlight non-significant fold changes in the heatmap.

subset_xaxis : list, optional (The default is None)
Subset x-axis before plotting. Pass in a list of categories. eg- subset_xaxis = ['CelltypeA', 'CellTypeB'].

subset_yaxis : list, optional (The default is None)
Subset y-axis before plotting. Pass in a list of categories. eg- subset_yaxis = ['ROI_1', 'ROI_5'].

cmap : string, optional (The default is vlag)
Color map. Can be a name or a Colormap instance (e.g. 'magma', 'viridis').

log : bool, optional (The default is True)
Convert foldchange to log2 scale.

center : float, optional (The default is 0)
The center value to be used in heatmap.

invert_axis : bool, optional (The default is None)
Flip the axis of the plot.

parallel_coordinates_color : list, optional (The default is None)
Custom colors for each category.

xticks_rotation : int, optional (The default is 90)
Angle the x-axis ticks.

matplotlib_bbox_to_anchor : tuple, optional (The default is (1.04,1))
Bounding box argument used along with matplotlib_legend_loc to control the legend location when using the matplotlib method.

matplotlib_legend_loc : int/string, optional (The default is upper left)
Location of legend used along with matplotlib_bbox_to_anchor to control the legend location when using the matplotlib method.

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

**kwargs : Additional keyword arguments passed to:
1) Pandas DataFrame.parallel_coordinates()) when using the parallel_coordinates method.
2) sns.clustermap() when using the heatmap method.

Returns

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

Example

# Heatmap of foldchnage
sm.pl.foldchange (adata, label='foldchange', method='heatmap',
                  p_val=0.05, nonsig_color='grey',
                  cmap = 'vlag', log=True, center=0, linecolor='black',linewidths=0.7,
                  vmin=-5, vmax=5, row_cluster=False)

# Parallel_coordinates plot of the foldchanges
foldchange (adata, label='foldchange', 
            log=True, method='parallel_coordinates', invert_axis=True,
            parallel_coordinates_color=['black','blue','green','red','#000000'],
            matplotlib_bbox_to_anchor=(1.04,1),
            matplotlib_legend_loc='upper left',
            xticks_rotation=90,
            return_data = False