anndata_fcs#

Attributes#

__version__

Functions#

`anndata_to_fcs`(adata)	Create fcs object from anndata.
`fcs_to_anndata`(fdata[, include_metadata])	Converts FlowData instance to AnnData object.
`fcs_to_dataframe`(fdata)	Converts FlowData instance to pandas DataFrame.
`gate_polygon`(fdata, x, y, polygon)	Gate channel `x` and `y` of FlowData instance with polygon.
`gate_polygon_subset`(fdata, x, y, polygon)	Gating polygon on flow data object and returning subset.
`scatter`(data, x, y[, xscale, yscale, density, gates, ...])	Plot scatter from FCS data.

Package Contents#

anndata_fcs.__version__: str = '0.1.0'#

anndata_fcs.anndata_to_fcs(adata)#

Create fcs object from anndata.

Parameters:: adata (anndata.AnnData) – AnnData object to convert.
Returns:: FlowData instance.
Return type:: flowio.FlowData
Raises:: AssertionError – If array conversion fails.

anndata_fcs.fcs_to_anndata(fdata, include_metadata=True)#

Converts FlowData instance to AnnData object.

Parameters:

fdata (flowio.FlowData) – FlowData instance to convert.
include_metadata (bool, optional) – If True is adds to FCS file meta data and .uns of the AnnData object.

Returns:

AnnData object.

Return type:

anndata.AnnData

anndata_fcs.fcs_to_dataframe(fdata)#

Converts FlowData instance to pandas DataFrame.

Parameters:: fdata (flowio.FlowData) – FlowData instance to convert.
Returns:: Pandas dataframe.
Return type:: pandas.DataFrame

anndata_fcs.gate_polygon(fdata, x, y, polygon)#

Gate channel x and y of FlowData instance with polygon.

Parameters:

fdata (flowio.FlowData) – FlowData instance to gate.
x (str) – Channel name for x coordinate.
y (str) – Channel name for y coordinate.
polygon (collections.abc.Sequence[collections.abc.Sequence[Union[int, float]]]) – Points of polygon with structure [[x1, y1], [xn, yn], ...].

Returns:

List of boolean with length of events per channel, where True indicated that point is inside the polygon.

Return type:

collections.abc.Sequence[bool]

anndata_fcs.gate_polygon_subset(fdata, x, y, polygon)#

Gating polygon on flow data object and returning subset.

Parameters:

fdata (flowio.FlowData) – FlowData instance to gate.
x (str) – Channel name for x coordinate.
y (str) – Channel name for y coordinate.
polygon (collections.abc.Sequence[collections.abc.Sequence[Union[int, float]]]) – Points of polygon with structure [[x1, y1], [xn, yn], ...].

Returns:

Subset on fdata object, only containing events inside of polygon.

Return type:

flowio.FlowData

anndata_fcs.scatter(data, x, y, xscale='log', yscale='log', density=False, gates=None, gate_color='black', highlight=None, highlight_color='red', color='black', ax=None, figsize=(5, 5))#

Plot scatter from FCS data.

Parameters:

data (Union[pandas.DataFrame, flowio.FlowData, anndata.AnnData]) – Event data. Argument can be DataFrame, AnnData or FlowData instance.
x (str) – Channel name for x coordinate.
y (str) – Channel name for y coordinate.
xscale (Literal["linear", "log", "symlog", "logit"], optional) – Scale of x axis. Defaults to log.
yscale (Literal["linear", "log", "symlog", "logit"], optional) – Scale of y axis. Defaults to log.
density (bool, optional) – Show denity as color. Defaults to False. scipy is required for this option.
gates (Optional[Dict[str, collections.abc[collections.abc[Union[int, float]]]]], optional) – Dict of gates, where the key indicated to name of the gate and the value describes to polygon. Defaults to None.
gate_color (str, optional) – Color of gate. Defaults to "black".
highlight (Optional[List[bool]], optional) – List of events to highlight. Defaults to None.
highlight_color (str, optional) – Color of events. Defaults to "red",
color (str) – Color of default event. Defaults to "black".
ax (Optional[matplotlib.axes.Axes], optional) – Matplotlib axes. Default to None.
figsize (Tuple[int, int], optional) – Figure size. Defaults to (5, 5).

Returns:

Axes instance.

Return type:

matplotlib.axes.Axes

Raises:

NotImplementedError – If data if other type than DataFrame, AnnData oder FlowData.
ImportError – If denity=True and scipy is not installed.
AssertionError – If length of highlight does not match with length of data.
AssertionError – If x and y gate boundaries could not be calculated.