dimensionality_reduction {CytobankAPI}

DimensionalityReduction Endpoints

Description

Interact with DimensionalityReduction advanced analyses using these endpoints.

Usage

## S4 method for signature 'UserSession,DimensionalityReduction'
dimensionality_reduction.copy_settings(
  UserSession,
  dimensionality_reduction,
  output = "default",
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession,DimensionalityReduction'
dimensionality_reduction.delete(
  UserSession,
  dimensionality_reduction,
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
dimensionality_reduction.list(
  UserSession,
  experiment_id,
  analysis_type,
  output = "default",
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession'
dimensionality_reduction.new(
  UserSession,
  experiment_id,
  analysis_name,
  analysis_type,
  timeout = UserSession@long_timeout
)

## S4 method for signature 'UserSession,DimensionalityReduction'
dimensionality_reduction.rename(
  UserSession,
  dimensionality_reduction,
  analysis_name,
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession,DimensionalityReduction'
dimensionality_reduction.run(
  UserSession,
  dimensionality_reduction,
  output = "default",
  timeout = UserSession@long_timeout
)

## S4 method for signature 'UserSession'
dimensionality_reduction.show(
  UserSession,
  experiment_id,
  analysis_id,
  analysis_type,
  timeout = UserSession@short_timeout
)

## S4 method for signature 'UserSession,DimensionalityReduction'
dimensionality_reduction.status(
  UserSession,
  dimensionality_reduction,
  output = "default",
  timeout = UserSession@long_timeout
)

## S4 method for signature 'UserSession,DimensionalityReduction'
dimensionality_reduction.update(
  UserSession,
  dimensionality_reduction,
  timeout = UserSession@long_timeout
)

Arguments

UserSession

Cytobank UserSession object

dimensionality_reduction

Cytobank DimensionalityReduction object

output

character representing the output format [optional]
- dimensionality_reduction.list, dimensionality_reduction.run, dimensionality_reduction.status : ("default", "raw")

timeout

integer representing the request timeout time in seconds [optional]

experiment_id

integer representing an experiment ID

analysis_type

character representing the Dimensionality Reduction type (tSNE-CUDA, opt-SNE, UMAP, or viSNE)

analysis_name

character the name of the Dimensionality Reduction analysis

analysis_id

integer representing the Dimensionality Reduction analysis ID

Details

dimensionality_reduction.copy_settings Copy DimensionalityReduction advanced analysis settings from an experiment and returns a DimensionalityReduction object.

dimensionality_reduction.delete Delete a DimensionalityReduction advanced analysis from an experiment.

dimensionality_reduction.list List all DimensionalityReduction advanced analyses from an experiment. Outputs a dataframe [default] or list with all fields present.
- Optional output parameter, specify one of the following: ("default", "raw")

dimensionality_reduction.new Create a new DimensionalityReduction advanced analysis from an experiment and returns a DimensionalityReduction object.

dimensionality_reduction.rename Rename a DimensionalityReduction advanced analysis from an experiment and returns the new name.

dimensionality_reduction.run Run a DimensionalityReduction advanced analysis from an experiment.

dimensionality_reduction.show Show DimensionalityReduction advanced analysis details from an experiment and returns a DimensionalityReduction object.

dimensionality_reduction.status Show the status of a DimensionalityReduction advanced analysis from an experiment.

dimensionality_reduction.update Update a DimensionalityReduction advanced analysis from an experiment and returns the new DimensionalityReduction object.

Examples

## Not run: # Authenticate via username/password
cyto_session <- authenticate(site="premium", username="cyril_cytometry", password="cytobank_rocks!")
# Authenticate via auth_token
cyto_session <- authenticate(site="premium", auth_token="my_secret_auth_token")

# cyto_dimensionality_reduction refers to a DimensionalityReduction object that is created from
DimensionalityReduction endpoints
#   examples: dimensionality_reduction.new, dimensionality_reduction.show (see details section for
more)

## End(Not run)
## Not run: dimensionality_reduction.copy_settings(cyto_session,
 dimensionality_reduction=cyto_dimensionality_reduction)

## End(Not run)
## Not run: dimensionality_reduction.delete(cyto_session,
dimensionality_reduction=cyto_dimensionality_reduction)

## End(Not run)
## Not run: # Dataframe of all DimensionalityReduction advanced analyses with all fields present
dimensionality_reduction.list(cyto_session, 22, "viSNE")

# Raw list of all DimensionalityReduction advanced analyses with all fields present
dimensionality_reduction.list(cyto_session, 22, "viSNE", output="raw")

## End(Not run)
## Not run: dimensionality_reduction.new(cyto_session, 22,
analysis_name="My new DimensionalityReduction analysis", "UMAP")

## End(Not run)
## Not run: dimensionality_reduction.rename(cyto_session,
dimensionality_reduction=cyto_dimensionality_reduction,
analysis_name="My updated DimensionalityReduction name")

## End(Not run)
## Not run: dimensionality_reduction.run(cyto_session,
dimensionality_reduction=cyto_dimensionality_reduction)

## End(Not run)
## Not run: dimensionality_reduction.show(cyto_session, 22, analysis_id=2, "opt-SNE")

## Not run: dimensionality_reduction.status(cyto_session,
dimensionality_reduction=cyto_dimensionality_reduction)

## End(Not run)
## Not run: dimensionality_reduction.update(cyto_session,
dimensionality_reduction=cyto_dimensionality_reduction)

## End(Not run)