Welcome to good-neighbors’ documentation!¶

good-neighbors¶

Identify neighborhoods based on local cell populations.

class goodneighbors.GoodNeighbors(h5path, location='', mode='r', microns_per_pixel=nan)[source]¶

Class for executing and storing the neighborhood analysis

Properties:

microns_per_pixel:
	(int) set in initialization
radius:	(float) pixel size of radius, set by set_neighborhood_fractions via the radius_um (in microns)
groupby:	(list) of cells fields who as a group can identify image frames
h5path:	(str) location of the h5path storing things
location:	(str) subdirectory in the h5object

cells¶

Access the pandas.DataFrame stored in the h5 object and return it

Returns:	(pandas.DataFrame)

measure_distance()[source]¶: Calculate the distance and store it in the cache

plot_counts_per_radius(min_radius=0, max_radius=150, step_radius=2)[source]¶

set_cells(df, groupby)[source]¶

Define the cells as a pandas.DataFrame

Inputs:

df:	(pandas.DataFrame) Must have columns defined `['cell_index','x','y','phenotype_label']`
groupby:	(list) List of fields that will group the pandas.DataFrame by image frame