visne {CytobankAPI}

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))