visne: viSNE Endpoints

In CytobankAPI: Cytobank API Wrapper for R

viSNE Endpoints

Description

Interact with viSNE advanced analyses using these endpoints.

Usage

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

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

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

## S4 method for signature 'UserSession'
visne.new(
  UserSession,
  experiment_id,
  visne_name,
  timeout = UserSession@long_timeout
)

## S4 method for signature 'UserSession,viSNE'
visne.rename(
  UserSession,
  visne,
  visne_name,
  timeout = UserSession@short_timeout
)

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

## S4 method for signature 'UserSession'
visne.show(
  UserSession,
  experiment_id,
  visne_id,
  timeout = UserSession@short_timeout
)

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

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

visne.helper.set_populations(visne, population_id = NA, fcs_files = NA)

Arguments

UserSession	Cytobank UserSession object
visne	Cytobank viSNE object
output	character representing the output format [optional] - visne.list, visne.run, visne.status : ("default", "raw")
timeout	integer representing the request timeout time in seconds [optional]
experiment_id	integer representing an experiment ID
visne_name	character representing a new viSNE name
visne_id	integer representing a viSNE ID
population_id	integer representing a population gate set ID
fcs_files	vector/list of integers representing a list of FCS file IDs

Details

visne.copy_settings Copy viSNE advanced analysis settings from an experiment and returns a viSNE object.

visne.delete Delete a viSNE advanced analysis from an experiment.

visne.list List all viSNE 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")

visne.new Create a new viSNE advanced analysis from an experiment and returns a viSNE object.

visne.rename Rename a viSNE advanced analysis from an experiment and returns a viSNE object.

visne.run Run a viSNE advanced analysis from an experiment.

visne.show Show viSNE advanced analysis details from an experiment and returns a viSNE object.

visne.status Show the status of a viSNE advanced analysis from an experiment.

visne.update Update a viSNE advanced analysis from an experiment and returns the new viSNE object.

visne.helper.set_populations Set viSNE advanced analysis populations to be selected from an experiment and returns the new viSNE object with the new population selections. The population provided will be overwritten by the newly selected FCS files provided.

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_visne refers to a viSNE object that is created from viSNE endpoints
#   examples: visne.new, visne.show (see details section for more)

## End(Not run)
## Not run: visne.copy_settings(cyto_session, visne=cyto_visne)

## Not run: visne.delete(cyto_session, visne=cyto_visne)

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

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

## End(Not run)
## Not run: visne.new(cyto_session, 22, visne_name="My new viSNE analysis")

## Not run: visne.rename(cyto_session, visne=cyto_visne, visne_name="My updated viSNE name")

## Not run: visne.run(cyto_session, visne=cyto_visne)

## Not run: visne.show(cyto_session, 22, visne_id=2)

## Not run: visne.status(cyto_session, visne=cyto_visne)

## Not run: visne.update(cyto_session, visne=cyto_visne)

## Not run: visne.helper.set_populations(visne=cyto_visne, population_id=1, fcs_files=c(1,2,3))

CytobankAPI documentation built on April 21, 2023, 9:08 a.m.