FlowSOM-class: S4 FlowSOM Class
In CytobankAPI: Cytobank API Wrapper for R

FlowSOM-class

R Documentation

S4 FlowSOM Class

Description

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

Value

A FlowSOM advanced analysis object

Slots

attachment_id: numeric representing the FlowSOM attachment to the source experiment containing the FlowSOM results
author: character representing the author of the FlowSOM analysis
auto_seed: logical representing whether to set an auto seed value or not
canceled: logical representing whether or not the FlowSOM analysis is canceled
channels_to_plot: list representing short channel IDs corresponding to channels to output channel-colored MST plots, learn more about FlowSOM PDF output
clustering_method: character representing the clustering method
- choose from the following : ("consensus" [default], "hierarchical", "kmeans")
cluster_size_type: character representing the cluster size type, learn more about FlowSOM PDF output
- choose from the following : ("both", "fixed", "relative" [default])
completed: logical representing whether or not the FlowSOM analysis is complete
created_experiment: numeric representing the experiment that gets created from the FlowSOM analysis
desired_events_per_file: numeric representing the number of desired events per file if event_sampling_method is set to equal, learn more about FlowSOM event sampling methods
desired_total_events: numeric representing the total desired number of events to sample amongst all selected files if event_sampling_method is set to proportional, learn more about FlowSOM event sampling methods
event_sampling_method: character representing the FlowSOM sampling method, learn more about FlowSOM event sampling methods
- choose from the following : ("all", "equal" [default], "proportional")
expected_clusters: numeric representing the number of expected clusters, learn more about choosing target number of clusters for FlowSOM
expected_metaclusters: numeric representing the expected number of metaclusters learn more about choosing target number of metaclusters for FlowSOM
external_som_analysis_info: character representing FlowSOM analysis information
external_som_analysis_id: character representing the ID of a corresponding FlowSOM analysis ID if som_creation_method set to "import_existing"
external_som_attachment_id: character representing the ID of a corresponding completed FlowSOM analysis if som_creation_method is set to import_existing
fcs_files: list of integers or character representing a list of FCS file IDs
final_result: character representing whether or not the FlowSOM analysis is successful
fixed_cluster_size: integer representing fixed cluster size if cluster_size_type set to "fixed" or "both"learn more about FlowSOM PDF output
flowsom_id: numeric representing the FlowSOM analysis ID
gate_set_names_to_label: list of character representing populations to label in the population pie plots, learn more about FlowSOM PDF output
iterations: numeric representing the number of times FlowSOM processes the dataset using its step-wise optimization algorithm, learn more about iterations in FlowSOM
max_relative_cluster_size: numeric representing the max relative cluster size (only applicable if cluster_size_type set to "relative" or "both", learn more about FlowSOM PDF output
normalize_scales: logical representing whether or not to normalize scales
num_events_to_actually_sample: numeric representing the events actually sampled
num_fcs_files: numeric representing the number of FCS files
output_file_type: character representing the output file type
- choose from the following : ("both", "pdf" [default], "png")
population_id: integer representing a population gate set ID
random_seed: numeric representing the seed value learn more about setting the seed for FlowSOM
show_background_on_legend: logical representing whether or not to show background on legend, learn more about FlowSOM PDF output
show_background_on_channel_colored_msts: logical representing whether or not to show background on channel colored MSTs, learn more about FlowSOM PDF output
show_background_on_population_pies: logical representing whether or not to show background on population pies, learn more about FlowSOM PDF output
som_creation_method: character representing the FlowSOM creation method, learn more about SOM creationg methods for FlowSOM
- choose from the following : ("create_new" [default], "import_existing")
type: character