UMAP-class: S4 UMAP Class
In CytobankAPI: Cytobank API Wrapper for R
UMAP-class R Documentation
S4 UMAP Class
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_channelslist 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_outlierslogical 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_filenumeric representing the number of desired events per file
desired_total_eventsnumeric representing the number of desired total events per file
event_sampling_methodcharacter representing the name of event sampling method will be used, learn more about Event Sampling for Dimensionality Reduction analysis
fcsfile_idslist representing the fcs file ids
gateset_idnumeric representing the selected gate id
min_distancenumeric the effective minimum distance between embedded points, learn more about minimum distance for UMAP analysis
num_neighborsnumeric 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_scaleslogical representing whether or not to normalize scales
CytobankAPI documentation built on April 21, 2023, 9:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| UMAP-class | R Documentation |
S4 UMAP Class
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_channelslist 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_outlierslogical 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_filenumeric representing the number of desired events per file
desired_total_eventsnumeric representing the number of desired total events per file
event_sampling_methodcharacter representing the name of event sampling method will be used, learn more about Event Sampling for Dimensionality Reduction analysis
fcsfile_idslist representing the fcs file ids
gateset_idnumeric representing the selected gate id
min_distancenumeric the effective minimum distance between embedded points, learn more about minimum distance for UMAP analysis
num_neighborsnumeric 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_scaleslogical representing whether or not to normalize scales
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.