Updating general CITRUS settings

Directly update CITRUS settings via their slot names.

The following slots can be updated directly:

• Required settings:

  • population_id
    • gateSetId from [email protected]_populations
  • channels: can be set as a list of channel IDs or a list of channel long names (long names must correlate to a unique short channel name)
  • statistics_channels (for medians mode only)
    • file_grouping (see the next section for how to update CITRUS file grouping)

• Optional settings (defaults in parentheses):

  • compensation_id: (experiment-wide compensation)
  • association_models: (“pamr”), sam”, and/or “glmnet”
  • cluster_characterization: (“abundances”) or “medians”
  • event_sampling_method: (“equal”) or “max-per-file”
  • events_per_file (5000 or the number in the smallest file, if less than 5000)
  • minimum_cluster_size (5)
  • cross_validation_folds (5)
  • false_discovery_rate (1)
  • normalize_scales: TRUE or (FALSE)
  • plot_theme: (“white”) or “black”

# Set association models, plot theme and compensation
CITRUS_object@association_models <- c("sam", "pamr", "glmnet")
CITRUS_object@plot_theme <- "black"
CITRUS_object@compensation_id <- 22

# Bulk update the changes made to the CITRUS object
CITRUS_object <- citrus.update(cyto_session, CITRUS_object)

Updating CITRUS file grouping

The core functionality of CITRUS is establishing biological explanations for why samples between two or more groups differ from each other. CITRUS file grouping is used to categorize different files into these groups. There is 1 important setting to pay attention to:

• group_name: the group that each file is associated with

  • The minimum number of samples per group is three. However, for more robust statistical analysis and to avoid spurious results, at least eight samples are recommended per group (see documentation for more information here)

  • There must be at least 2 groups in order to run a CITRUS analysis

Directly update CITRUS file grouping data.

# Set 'file1.fcs' through 'file4.fcs' to 'Group 1' and 'file5.fcs' through 'file8.fcs' to 'Group 2', exclude 'file9.fcs' from analysis
CITRUS_object@file_grouping[CITRUS_object@file_grouping$id <= 44856,]$group_name <- "Group 1"
CITRUS_object@file_grouping[is.element(c(44857, 44858, 44859, 44860), CITRUS_object@file_grouping$id),]$group_name <- "Group 2"

View(CITRUS_object@file_grouping)

Learn more about CITRUS file grouping.

Updating general FlowSOM settings

Directly update FlowSOM settings via their slot names.

The following slots can be updated directly:

• Basic settings:
  • population_id: gateSetId from [email protected]_populations
  • channels: can be set as a list of channel IDs or a list of channel long names (long names must correlate to a unique short channel name)
  • fcs_files
  • random_seed
  • compensation_id: must match experiment-wide compensation
• Event sampling settings:
  • event_sampling_method: “equal”, “proportional”, or “all”
  • desired_events_per_file: for equal sampling
  • desired_total_events: for proportional sampling
• Algorithm settings (default in parentheses):
  • som_creation_method: (“create_new”) or “import_existing”
    • external_som_analysis_id: if importing existing SOM, character of source FlowSOM ID
  • clustering_method: (“consensus”), “hclust”, or “kmeans”
  • expected_metaclusters (10)
  • expected_clusters (100)
  • iterations (10)
• Transformations settings (default in parentheses):
  • normalize_scales: TRUE or (FALSE)
• PDF output settings (default in parentheses):
  • channels_to_plot: channels can be set as a list of channel IDs or a list of channel long names (long names must correlate to a unique short channel name)
  • cluster_size_type: (“relative”), “fixed” or “both”
  • fixed_cluster_size (8)
  • max_relative_cluster_size (15)
  • gate_set_names_to_label: populations for pie charts
  • output_file_type: (“pdf”), “png” or “both”
  • Toggle metacluster background on plots: TRUE or FALSE
    • show_background_on_legend: (FALSE)
    • show_background_on_channel_colored_msts (FALSE)
    • show_background_on_population_pies (TRUE)

If the required channels, fcs_files and random_seed slots are not present, updates will not occur to the FlowSOM analysis.

# Set a clustering method and target number of nodes
FlowSOM_object@clustering_method <- "kmeans"
FlowSOM_object@num_expected_clusters <- 144

# Update FCS file selection to the first 5 files
FlowSOM_object@fcs_files <- FlowSOM_object@.available_files$id[1:5]

# Update channel selection
FlowSOM_object@channels <- list("CD3", "CD4")

# Bulk update the changes made to the FlowSOM object
FlowSOM_object <- flowsom.update(cyto_session, FlowSOM_object)

Updating general SPADE settings

Directly update SPADE settings via their slot names.

The following slots can be updated directly:

• Required settings:
  • population_id
  • channels: channels can be set as a list of channel IDs or a list of channel long names (long names must correlate to a unique short channel name)
• Additional settings if changing from default (in parentheses):
  • compensation (experiment-wide compensation)
  • target_number_nodes (200)
  • down_sampled_events_target (10)
  • down_sampled_events_type (“percent”) or “absoluteNumber”
  • fold_change_groups: see the next section for how to update SPADE fold change groups

# Set a new population, target number of nodes, and compensation
SPADE_object@population_id <- 2
SPADE_object@target_number_nodes <- 150
SPADE_object@compensation_id <- 22

# Update channels
channel_ids_list <- list(2, 3, 5, 8)
SPADE_object@channels <- channel_ids_list

# Update channels by long channel names
channel_names_list <- list("channel1", "channel2", "channel3")
SPADE_object@channels <- channel_names_list

# Bulk update the changes made to the SPADE object
SPADE_object <- spade.update(cyto_session, SPADE_object)

SPADE_object@population_id
#> [1] 2
SPADE_object@target_number_nodes
#> [1] 150
SPADE_object@compensation_id
#> [1] 22
SPADE_object@channels
#> [[1]]
#> [1] "channel1"
#>
#> [[2]]
#> ...

Updating SPADE fold change groups

SPADE fold change groups are used to categorize different files into separate collections that will be compared amongst each other. There are 2 important settings to pay attention to:

1. group_name: The group a specific file belongs to
2. baseline: The file(s) used as the baseline in order to calculate fold change

Directly update SPADE fold change groups data.

# Set 'file6.fcs' and 'file7.fcs' as the baseline for 'Group 1'
SPADE_object@fold_change_groups[grep("my_file6|my_file7", 
    SPADE_object@fold_change_groups$name),]$baseline <- TRUE

# Set 'file2.fcs', 'file4.fcs', and 'file8.fcs' as part of 'Group 2', and set 'file2.fcs' as the baseline
SPADE_object@fold_change_groups[grep("file2|file4|file8", 
    SPADE_object@fold_change_groups$name),]$group_name <- "Group 2"
SPADE_object@fold_change_groups[SPADE_object@fold_change_groups$name=="file2.fcs",]$baseline <- TRUE

View(SPADE_object@fold_change_groups)

Learn more about SPADE fold change groups.

Updating general viSNE settings

Directly update viSNE settings via their slot names.

The following slots can be updated directly:

• sampling_target_type

• sampling_total_count

• channels

  • channels can be set as a list of channel IDs or a list of channel long names (long names must correlate to a unique short channel name)

• compensation_id

• iterations

• perplexity

• theta

• seed

The following slots must be updated via helper functions:

• population_selections (see the next section for how to update viSNE population selections)

  • visne.helper.set_populations

# Set a new sampling target type, sampling total count, and compensation
viSNE_object@sampling_target_type <- "equal"
viSNE_object@sampling_total_count <- 150000
viSNE_object@compensation_id <- 22

# Bulk update the changes made to the viSNE object
viSNE_object <- visne.update(cyto_session, viSNE_object)

Updating viSNE population selections

Adding viSNE population selections is slightly more difficult because the same file can be used in the analysis in combination with multiple populations. Because of this complexity, the visne.helper.set_populations helper function is used to set files for a selected population.

Parameters for visne.helper.set_populations:

1. visne: The viSNE object to set populations for
2. population_id: The gate set ID for the specified population (different than the actual population ID, and can be obtained by looking at the .available_populations slot)
3. fcs_files: A vector/list of FCS files to set for the population

Set files for a specific population through the visne.helper.set_populations helper function.

Setting files for a specific population will overwrite the files previously set for the population in question.

# Set files for different populations
viSNE_object <- visne.helper.set_populations(viSNE_object, population_id=1, fcs_files=c(44853))
viSNE_object <- visne.helper.set_populations(viSNE_object, population_id=2, fcs_files=c(44867,44868))
viSNE_object <- visne.helper.set_populations(viSNE_object, population_id=4, fcs_files=unlist(visne@.available_files[grep("file4|file5|file6", visne@.available_files$filename),]$id))
# Overwrite 'population_id=2' FCS file selection, note that 'file1.fcs' and 'file2.fcs' are in both 'Population 1', as well as 'Population 2'
viSNE_object <- visne.helper.set_populations(viSNE_object, population_id=2, fcs_files=c(44854,44855, 44853, 44867))

# Update the changes made to viSNE population selections
viSNE_object <- visne.update(cyto_session, viSNE_object)

View(viSNE_object@population_selections)

Learn more about selecting viSNE populations.

Setting up a new analysis run using one of the algorithms that are available in Dimensionality Reduction Suite

The following example shows how to set up and launch a tSNE-CUDA analysis run.

# create a new dimensionality reduction analysis object and set the analysis type to be tSNE-CUDA
dimensionality_reduction_object<-dimensionality_reduction.new(cyto_session, experiment_id=22, analysis_name = 'use API to launch a tSNEcuda run', analysis_type = 'tSNE-CUDA')

# select clustering channels
dimensionality_reduction_object@clustering_channels<-list('CD4','CD8','CD3')

# Bulk update the change
dimensionality_reduction_object<-dimensionality_reduction.update(cyto_session,dimensionality_reduction_object)

# Launch the configured analysis run
dimensionality_reduction.run(cyto_session,dimensionality_reduction_object)

# Check the status of the launched analysis run
dimensionality_reduction.status(cyto_session,cyto_tsnecuda)

Updating general settings for the algorithms in Dimensionality Reduction Suite

Directly update settings via their slot names.

The following slots can be updated directly:

• tSNE-CUDA, opt-SNE and UMAP:
  • event_sampling_method
  • desired_total_events
  • clustering_channels
    • channels can be set as a list of channel IDs or a list of channel long names (long names must correlate to a unique short channel name)
    • channel names can be obtained by looking at the .available_channels slot
  • normalize_scales
• Additional slots for tSNE-CUDA:
  • perplexity
  • iterations
  • auto_iterations
  • learning_rate
  • auto_learning_rate
  • early_exaggeration
• Additional slots for opt-SNE:
  • perplexity
  • auto_learning_rate
  • learning_rate
  • early_exaggeration
  • max_iterations
  • random_seed
• Additional slots for UMAP:
  • collapse_outliers
  • min_distance
  • num_neighbors

# Set a new sampling target type, sampling total count, and compensation
dimensionality_reduction_object@event_sampling_method <- "equal"
dimensionality_reduction_object@desired_total_events <- 150000

# Bulk update the changes made to the dimensionality reduction object
dimensionality_reduction_object <- dimensionality_reduction.update(cyto_session, dimensionality_reduction_object)