UMAP-class: S4 UMAP Class

Description Value Slots

Description

A UMAP object that holds pertinent UMAP advanced analysis run information. This class should never be called explicitly. If a user would like to create a new Cytobank UMAP object, utilize the dimensionality_reduction.new function, or any other UMAP endpoints that return UMAP objects documented in the 'Details' section.

Value

A UMAP advanced analysis object

Slots

clustering_channels

list the channels selected for the Dimensionality Reduction analysis, this can be either a list of short channel IDs (integer) OR long channel names (character)

collapse_outliers

logical Dimension values that are significant outliers (z-score > 3) will be collapsed to be equal to the min or max value. Try this if you observe that most of the data appears squished within small region

desired_events_per_file

numeric representing the number of desired events per file

desired_total_events

numeric representing the number of desired total events per file

event_sampling_method

character representing the name of event sampling method will be used, learn more about Event Sampling for Dimensionality Reduction analysis

fcsfile_ids

list representing the fcs file ids

gateset_id

numeric representing the selected gate id

min_distance

numeric the effective minimum distance between embedded points, learn more about minimum distance for UMAP analysis

num_neighbors

numeric the size of local neighborhood (in terms of number of neighboring sample points) used for manifold approximation, learn more about number of neighbors for UMAP analysis

normalize_scales

logical representing whether or not to normalize scales


CytobankAPI documentation built on Oct. 4, 2021, 9:07 a.m.