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FACSPy
Installation
FACSPy API Reference
Tools
FACSPy.tl.mfi
FACSPy.tl.fop
FACSPy.tl.gate_frequencies
FACSPy.tl.gate_frequencies_mem
FACSPy.tl.umap
FACSPy.tl._compute_umap
FACSPy.tl.tsne
FACSPy.tl._compute_tsne
FACSPy.tl.diffmap
FACSPy.tl._compute_diffmap
FACSPy.tl.pca
FACSPy.tl._compute_pca
FACSPy.tl.parc
FACSPy.tl.flowsom
FACSPy.tl.leiden
FACSPy.tl.phenograph
FACSPy.tl.neighbors
FACSPy.tl.pca_samplewise
FACSPy.tl.tsne_samplewise
FACSPy.tl.mds_samplewise
FACSPy.tl.umap_samplewise
FACSPy.tl.correct_expression
FACSPy.tl.harmony_integrate
FACSPy.tl.scanorama_integrate
Plotting
FACSPy.pl.biax
FACSPy.pl.fold_change
FACSPy.pl.cluster_frequency
FACSPy.pl.cluster_abundance
FACSPy.pl.marker_density
FACSPy.pl.mfi
FACSPy.pl.fop
FACSPy.pl.sample_correlation
FACSPy.pl.sample_distance
FACSPy.pl.pca_samplewise
FACSPy.pl.mds_samplewise
FACSPy.pl.tsne_samplewise
FACSPy.pl.umap_samplewise
FACSPy.pl.cofactor_distribution
FACSPy.pl.transformation_plot
FACSPy.pl.gating_strategy
FACSPy.pl.cell_counts
FACSPy.pl.gate_frequency
FACSPy.pl.expression_heatmap
FACSPy.pl.cluster_heatmap
FACSPy.pl.cluster_mfi
FACSPy.pl.cluster_fop
FACSPy.pl.marker_correlation
FACSPy.pl.metadata
FACSPy.pl.umap
FACSPy.pl.pca
FACSPy.pl.diffmap
FACSPy.pl.tsne
Model
FACSPy.ml.supervisedGating
FACSPy.ml.supervisedGating.gate_dataset
FACSPy.ml.supervisedGating.get_dataset
FACSPy.ml.supervisedGating.run_data_setup
FACSPy.ml.supervisedGating.sample_cells
FACSPy.ml.supervisedGating.setup_classifier
FACSPy.ml.supervisedGating.train
FACSPy.ml.supervisedGating.tune_hyperparameters
FACSPy.ml.unsupervisedGating
FACSPy.ml.unsupervisedGating.get_dataset
FACSPy.ml.unsupervisedGating.identify_populations
Dataset
FACSPy.dt.create_dataset
FACSPy.dt.transform
FACSPy.dt.calculate_cofactors
FACSPy.dt.CofactorTable
FACSPy.dt.CofactorTable.get_cofactor
FACSPy.dt.CofactorTable.rename_channel
FACSPy.dt.CofactorTable.select_channels
FACSPy.dt.CofactorTable.set_cofactor
FACSPy.dt.CofactorTable.set_cofactors
FACSPy.dt.CofactorTable.set_columns
FACSPy.dt.CofactorTable.to_df
FACSPy.dt.CofactorTable.write
FACSPy.dt.Metadata
FACSPy.dt.Metadata.annotate
FACSPy.dt.Metadata.get_factors
FACSPy.dt.Metadata.group_variable
FACSPy.dt.Metadata.rename_column
FACSPy.dt.Metadata.rename_values
FACSPy.dt.Metadata.select_channels
FACSPy.dt.Metadata.subset
FACSPy.dt.Metadata.to_df
FACSPy.dt.Metadata.write
FACSPy.dt.Panel
FACSPy.dt.Panel.get_antigens
FACSPy.dt.Panel.get_channels
FACSPy.dt.Panel.rename_antigen
FACSPy.dt.Panel.rename_channel
FACSPy.dt.Panel.select_channels
FACSPy.dt.Panel.to_df
FACSPy.dt.Panel.write
FACSPy.dt.create_empty_metadata
FACSPy.dt.create_panel_from_fcs
FACSPy.dt.FlowJoWorkspace
FACSPy.dt.FlowJoWorkspace.add_external_compensation
FACSPy.dt.DivaWorkspace
IO
FACSPy.save_dataset
FACSPy.read_dataset
Synchronization
FACSPy.sync.synchronize_dataset
FACSPy.sync.sample_ids_from_obs
FACSPy.sync.sample_ids_from_metadata
Utils
FACSPy.subset_gate
FACSPy.subset_fluo_channels
FACSPy.remove_unnamed_channels
FACSPy.remove_channel
FACSPy.equalize_groups
FACSPy.convert_gate_to_obs
FACSPy.rename_channel
FACSPy.convert_cluster_to_gate
Settings
FACSPy.FACSPyConfig
FACSPy.FACSPyConfig.default_categorical_cmap
FACSPy.FACSPyConfig.default_gate
FACSPy.FACSPyConfig.default_layer
FACSPy.FACSPyConfig.gate_aliases
FACSPy.FACSPyConfig.n_jobs
FACSPy.FACSPyConfig.tight_layout
FACSPy.FACSPyConfig.add_new_alias
Vignettes
Dataset Creation and Transformation
Dataset Gating: Unsupervised Gating
Data analysis: Fluorescence intensity and Frequency of Parents
Data Analysis: Cell frequency analysis
Data analysis: Samplewise Analysis
Data analysis: Single cell analysis
Data analysis: Interacting with R packages
The Panel object
The Metadata object
The CofactorTable object
The FACSPy dataset: Structure
The FACSPy dataset: Gate Handling
References
.rst
.pdf
FACSPy.ml.unsupervisedGating.get_dataset
Contents
unsupervisedGating.get_dataset()
FACSPy.ml.unsupervisedGating.get_dataset
#
unsupervisedGating.
get_dataset
(
)
#
Returns a
AnnData
object
Contents
unsupervisedGating.get_dataset()