cytoflow.utility package

cytoflow.utility

This package contains a bunch of utility functions to support the other modules in cytoflow. This includes numeric functions, algorithms, error handling, custom traits, custom matplotlib widgets, custom matplotlib scales, and docstring handling.

class cytoflow.utility.IterByWrapper(iterator, by)

Bases: object

Submodules

• cytoflow.utility.algorithms
• ci()
• percentiles()
• bootstrap()
• is_inside_sm()
• polygon_contains()
• resample()
• compute_connectivity_matrix()
• compute_identity_matrix()
• compute_consensus_matrix()
• valid_clustering_obj()
• cluster()
• ConsensusClustering
  • ConsensusClustering.cluster_range_
  • ConsensusClustering.consensus_k()
  • ConsensusClustering.fit()
  • ConsensusClustering.hist()
  • ConsensusClustering.cdf()
  • ConsensusClustering.area_under_cdf()
  • ConsensusClustering.change_in_area_under_cdf()
  • ConsensusClustering.best_k()
  • ConsensusClustering.plot_auc_cdf()
  • ConsensusClustering.plot_clustermap()
  • ConsensusClustering.plot_hist()
  • ConsensusClustering.plot_cdf()
  • ConsensusClustering.plot_change_area_under_cdf()
• ConsensusCluster
  • ConsensusCluster.fit()
  • ConsensusCluster.predict()
  • ConsensusCluster.predict_data()
• cytoflow.utility.custom_traits
• PositiveInt
  • PositiveInt.info_text
  • PositiveInt.validate()
• PositiveCInt
  • PositiveCInt.info_text
  • PositiveCInt.validate()
• PositiveFloat
  • PositiveFloat.info_text
  • PositiveFloat.validate()
• PositiveCFloat
  • PositiveCFloat.info_text
  • PositiveCFloat.validate()
• FloatOrNone
  • FloatOrNone.info_text
  • FloatOrNone.validate()
• CFloatOrNone
  • CFloatOrNone.info_text
  • CFloatOrNone.validate()
• UnitFloat
  • UnitFloat.validate()
• IntOrNone
  • IntOrNone.info_text
  • IntOrNone.validate()
• CIntOrNone
  • CIntOrNone.info_text
  • CIntOrNone.validate()
• ScaleEnum
  • ScaleEnum.info_text
  • ScaleEnum.get_default_value()
• Removed
  • Removed.get()
  • Removed.set()
• Deprecated
  • Deprecated.get()
  • Deprecated.set()
• ChangedStr
  • ChangedStr.error()
• cytoflow.utility.cytoflow_errors
• CytoflowError
• CytoflowOpError
• CytoflowViewError
• CytoflowWarning
• CytoflowOpWarning
• CytoflowViewWarning
• cytoflow.utility.docstring
• expand_class_attributes()
• expand_method_parameters()
• find_section()
• get_class_attributes()
• get_method_parameters()
• cytoflow.utility.fcswrite
• write_fcs()
• cytoflow.utility.hlog_scale
• HlogScale
  • HlogScale.b
  • HlogScale.name
  • HlogScale.inverse()
  • HlogScale.clip()
  • HlogScale.norm()
  • HlogScale.get_mpl_params()
• MatplotlibHlogScale
  • MatplotlibHlogScale.name
  • MatplotlibHlogScale.get_transform()
  • MatplotlibHlogScale.set_default_locators_and_formatters()
  • MatplotlibHlogScale.HlogTransform
    • MatplotlibHlogScale.HlogTransform.input_dims
    • MatplotlibHlogScale.HlogTransform.output_dims
    • MatplotlibHlogScale.HlogTransform.is_separable
    • MatplotlibHlogScale.HlogTransform.has_inverse
    • MatplotlibHlogScale.HlogTransform.transform_non_affine()
    • MatplotlibHlogScale.HlogTransform.inverted()
  • MatplotlibHlogScale.InvertedLogicleTransform
    • MatplotlibHlogScale.InvertedLogicleTransform.input_dims
    • MatplotlibHlogScale.InvertedLogicleTransform.output_dims
    • MatplotlibHlogScale.InvertedLogicleTransform.is_separable
    • MatplotlibHlogScale.InvertedLogicleTransform.has_inverse
    • MatplotlibHlogScale.InvertedLogicleTransform.transform_non_affine()
    • MatplotlibHlogScale.InvertedLogicleTransform.inverted()
• HlogMajorLocator
  • HlogMajorLocator.set_params()
  • HlogMajorLocator.tick_values()
  • HlogMajorLocator.view_limits()
• HlogMinorLocator
  • HlogMinorLocator.set_params()
  • HlogMinorLocator.tick_values()
• hlog_inv()
• hlog()
• KneeLocator
  • KneeLocator.transform_y()
  • KneeLocator.find_knee()
  • KneeLocator.plot_knee_normalized()
  • KneeLocator.plot_knee()
  • KneeLocator.elbow
  • KneeLocator.norm_elbow
  • KneeLocator.elbow_y
  • KneeLocator.norm_elbow_y
  • KneeLocator.all_elbows
  • KneeLocator.all_norm_elbows
  • KneeLocator.all_elbows_y
  • KneeLocator.all_norm_elbows_y
• cytoflow.utility.linear_scale
• LinearScale
  • LinearScale.name
  • LinearScale.inverse()
  • LinearScale.clip()
  • LinearScale.norm()
  • LinearScale.get_mpl_params()
• cytoflow.utility.log_scale
• LogScale
  • LogScale.name
  • LogScale.get_mpl_params()
  • LogScale.inverse()
  • LogScale.clip()
  • LogScale.norm()
• cytoflow.utility.logging_ext
• MplFilter
  • MplFilter.filter()
• cytoflow.utility.logicle_scale
• LogicleScale
  • LogicleScale.experiment
  • LogicleScale.channel
  • LogicleScale.condition
  • LogicleScale.statistic
  • LogicleScale.W
  • LogicleScale.M
  • LogicleScale.A
  • LogicleScale.r
  • LogicleScale.name
  • LogicleScale.inverse()
  • LogicleScale.clip()
  • LogicleScale.norm()
  • LogicleScale.get_mpl_params()
• MatplotlibLogicleScale
  • MatplotlibLogicleScale.name
  • MatplotlibLogicleScale.get_transform()
  • MatplotlibLogicleScale.set_default_locators_and_formatters()
  • MatplotlibLogicleScale.LogicleTransform
    • MatplotlibLogicleScale.LogicleTransform.input_dims
    • MatplotlibLogicleScale.LogicleTransform.output_dims
    • MatplotlibLogicleScale.LogicleTransform.is_separable
    • MatplotlibLogicleScale.LogicleTransform.has_inverse
    • MatplotlibLogicleScale.LogicleTransform.transform_non_affine()
    • MatplotlibLogicleScale.LogicleTransform.inverted()
  • MatplotlibLogicleScale.InvertedLogicleTransform
    • MatplotlibLogicleScale.InvertedLogicleTransform.input_dims
    • MatplotlibLogicleScale.InvertedLogicleTransform.output_dims
    • MatplotlibLogicleScale.InvertedLogicleTransform.is_separable
    • MatplotlibLogicleScale.InvertedLogicleTransform.has_inverse
    • MatplotlibLogicleScale.InvertedLogicleTransform.transform_non_affine()
    • MatplotlibLogicleScale.InvertedLogicleTransform.inverted()
• LogicleMajorLocator
  • LogicleMajorLocator.set_params()
  • LogicleMajorLocator.tick_values()
  • LogicleMajorLocator.view_limits()
• LogicleMinorLocator
  • LogicleMinorLocator.set_params()
  • LogicleMinorLocator.tick_values()
  • LogicleMinorLocator.view_limits()
• cytoflow.utility.minisom
• fast_norm()
• MiniSom
  • MiniSom.Y_HEX_CONV_FACTOR
  • MiniSom.get_weights()
  • MiniSom.get_euclidean_coordinates()
  • MiniSom.convert_map_to_euclidean()
  • MiniSom.activate()
  • MiniSom.winner()
  • MiniSom.update()
  • MiniSom.quantization()
  • MiniSom.random_weights_init()
  • MiniSom.pca_weights_init()
  • MiniSom.train()
  • MiniSom.train_random()
  • MiniSom.train_batch()
  • MiniSom.distance_map()
  • MiniSom.activation_response()
  • MiniSom.quantization_error()
  • MiniSom.quantization_history()
  • MiniSom.distortion_measure()
  • MiniSom.topographic_error()
  • MiniSom.win_map()
  • MiniSom.labels_map()
• TestMinisom
  • TestMinisom.setUp()
  • TestMinisom.test_inverse_decay_to_zero_function()
  • TestMinisom.test_linear_decay_to_zero_function()
  • TestMinisom.test_inverse_decay_to_one_function()
  • TestMinisom.test_linear_decay_to_one_function()
  • TestMinisom.test_asymptotic_decay_function()
  • TestMinisom.test_fast_norm()
  • TestMinisom.test_euclidean_distance()
  • TestMinisom.test_cosine_distance()
  • TestMinisom.test_manhattan_distance()
  • TestMinisom.test_chebyshev_distance()
  • TestMinisom.test_check_input_len()
  • TestMinisom.test_unavailable_neigh_function()
  • TestMinisom.test_unavailable_distance_function()
  • TestMinisom.test_gaussian()
  • TestMinisom.test_mexican_hat()
  • TestMinisom.test_bubble()
  • TestMinisom.test_triangle()
  • TestMinisom.test_win_map()
  • TestMinisom.test_win_map_indices()
  • TestMinisom.test_labels_map()
  • TestMinisom.test_activation_reponse()
  • TestMinisom.test_activate()
  • TestMinisom.test_distance_from_weights()
  • TestMinisom.test_quantization_error()
  • TestMinisom.test_topographic_error()
  • TestMinisom.test_hexagonal_topographic_error()
  • TestMinisom.test_quantization()
  • TestMinisom.test_distortion_measure()
  • TestMinisom.test_random_seed()
  • TestMinisom.test_train_batch()
  • TestMinisom.test_train_random()
  • TestMinisom.test_train_use_epochs()
  • TestMinisom.test_train_fixed_points()
  • TestMinisom.test_use_epochs_variables()
  • TestMinisom.test_random_weights_init()
  • TestMinisom.test_pca_weights_init()
  • TestMinisom.test_distance_map()
  • TestMinisom.test_pickling()
  • TestMinisom.test_callable_activation_distance()
  • TestMinisom.test_decay_function_value()
  • TestMinisom.test_sigma_decay_function_value()
• cytoflow.utility.scale
• IScale
  • IScale.name
  • IScale.experiment
  • IScale.channel
  • IScale.condition
  • IScale.statistic
  • IScale.data
  • IScale.inverse()
  • IScale.clip()
  • IScale.norm()
• ScaleMixin
• scale_factory()
• register_scale()
• set_default_scale()
• get_default_scale()
• cytoflow.utility.util_functions
• iqr()
• num_hist_bins()
• geom_mean()
• geom_sd()
• geom_sd_range()
• geom_sem()
• geom_sem_range()
• cartesian()
• sanitize_identifier()
• random_string()
• is_numeric()
• cov2corr()