Containers

FCMeasurement

FCMeasurement(ID[, datafile, readdata, ...]) A class for holding flow cytometry data from a single well or a single tube.
FCMeasurement.apply(func[, applyto, ...]) Apply func either to self or to associated data.
FCMeasurement.plot(channel_names[, kind, ...]) Plots the flow cytometry data associated with the sample on the current axis.
FCMeasurement.transform(transform[, ...]) Applies a transformation to the specified channels.
FCMeasurement.gate(gate[, apply_now]) Apply given gate and return new gated sample (with assigned data).
FCMeasurement.counts Returns total number of events.
FCMeasurement.get_data(**kwargs) Get the measurement data.
FCMeasurement.view_interactively([backend]) Loads the current sample in a graphical interface for drawing gates.
FCMeasurement.channel_names A tuple containing the channel names.
FCMeasurement.channels A DataFrame containing complete channel information
FCMeasurement.subsample(key[, order, ...]) Allows arbitrary slicing (subsampling) of the data.

FCPlate

FCOrderedCollection(ID, measurements, ...[, ...]) A dict-like class for holding flow cytometry samples that are arranged in a matrix.
FCPlate A dict-like class for holding flow cytometry samples that are arranged in a matrix.
FCPlate.from_files(ID, datafiles[, parser, ...]) Create an OrderedCollection of measurements from a set of data files.
FCPlate.from_dir(ID, path[, parser, ...]) Create a Collection of measurements from data files contained in a directory.
FCPlate.apply(func[, ids, applyto, ...]) Apply func to each of the specified measurements.
FCPlate.plot(channel_names[, kind, gates, ...]) Produces a grid plot with each subplot corresponding to the data at the given position.
FCPlate.transform(transform[, direction, ...]) Apply transform to each Measurement in the Collection.
FCPlate.gate(gate[, ID, apply_now]) Applies the gate to each Measurement in the Collection, returning a new Collection with gated data.
FCPlate.counts([ids, setdata, output_format]) Return the counts in each of the specified measurements.
FCPlate.dropna() Remove rows and cols that have no assigned measurements.
FCPlate.subsample(key[, order, auto_resize, ID]) Allows arbitrary slicing (subsampling) of the data.

Gates

ThresholdGate(threshold, channel, region[, name]) Passes all events above or below a given threshold.
IntervalGate(vert, channel, region[, name]) Passes all events either inside or outside the given interval.
QuadGate(vert, channels, region[, name]) Passes events in a given quadrant of a 2d-plot.
PolyGate(vert, channels[, region, name]) Passes all events that are either inside or outside the polygon.
FlowCytometryTools.core.gates.CompositeGate(...) Defines a composite gate that is generated by the logical addition of one or more gates.

Transformations

FlowCytometryTools.core.transforms.linear(x, ...) Rescale each channel to the new range as following:
FlowCytometryTools.core.transforms.hlog(x[, ...]) Base 10 hyperlog transform.
FlowCytometryTools.core.transforms.tlog(x[, ...]) Truncated log10 transform.