FlowSOM-class {CytobankAPI}

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