cytopy.data.population

When analysing single cell data we are ultimately interested in populations of cells. This module contains the Population class, which controls the data attaining to a single cell population. A FileGroup (see cytopy.data.fcs) can contain many Populations (which are embedded within the FileGroup).

Copyright 2020 Ross Burton

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Classes:

Population(*args, **kwargs)

A population of cells identified by either a gate, clustering or supervised algorithm.

Functions:

merge_gate_populations(left, right[, …])	Merge two Population’s.
merge_multiple_gate_populations(populations)	Merge multiple Population’s.
merge_non_geom_populations(populations, …)	Merge populations arising from classification or clustering.

class cytopy.data.population.Population(*args, **kwargs)

A population of cells identified by either a gate, clustering or supervised algorithm. Stores the index of events corresponding to a single population, where the index relates back to the primary data in the FileGroup in which a population is embedded.

population_name

name of population

Type

str, required

n

number of events associated to this population

Type

int

parent

name of parent population

Type

str, required, (default: “root”)

prop_of_parent

proportion of events as a percentage of parent population

Type

float, required

prop_of_total

proportion of events as a percentage of all events

Type

float, required

warnings

list of warnings associated to population

Type

list, optional

geom

PopulationGeometry (see cytopy.data.geometry) that defines the gate that captures this population.

Type

PopulationGeometry

definition

relevant for populations generated by a ThresholdGate; defines the source of this population e.g. “+” for a 1D threshold or “+-” for a 2D threshold

Type

str

index

numpy array storing index of events that belong to population

Type

numpy.ndarray

signature

average of a population feature space (median of each channel); used to match children to newly identified populations for annotating

Type

dict

source

Source of the population i.e. what method was used to generate it. Valid choices are: “gate”, “cluster”, “root”, or “classifier”

Type

str, required

cytopy.data.population.merge_gate_populations(left: cytopy.data.population.Population, right: cytopy.data.population.Population, new_population_name: Optional[str] = None)

Merge two Population’s. The indexes and signatures of these populations will be merged. The populations must have the same geometries.

Parameters

• left (Population) –

• right (Population) –

• new_population_name (str) –

Returns

Return type

Population

Raises

AssertionError – Invalid populations provided

cytopy.data.population.merge_multiple_gate_populations(populations: List[cytopy.data.population.Population], new_population_name: Optional[str] = None)

Merge multiple Population’s. The indexes and signatures of these populations will be merged. The populations must have the same geometries.

Parameters

• populations (list) –

• new_population_name (str) –

Returns

Return type

Population

Raises

AssertionError – Invalid populations provided

cytopy.data.population.merge_non_geom_populations(populations: list, new_population_name: str)

Merge populations arising from classification or clustering. Takes a list of Population objects and the name for the new population and merges their indexes, forming a new Population object.

Parameters

• populations (list) –

• new_population_name (str) –

Returns

Return type

Population

Raises

AssertionError – Invalid populations provided