citrus {CytobankAPI}

CITRUS Endpoints

Description

Interact with CITRUS advanced analyses using these endpoints.

Usage

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

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

## S4 method for signature 'UserSession,CITRUS'
citrus.download(
  UserSession,
  citrus,
  directory = getwd(),
  timeout = UserSession@long_timeout
)

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

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

## S4 method for signature 'UserSession,CITRUS'
citrus.rename(
  UserSession,
  citrus,
  citrus_name,
  timeout = UserSession@short_timeout
)

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

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

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

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

Arguments

UserSession

Cytobank UserSession object

citrus

Cytobank CITRUS object

output

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

timeout

integer representing the request timeout time in seconds [optional]

directory

character representing a specific directory to which the file will be downloaded (optional ending directory slash), if left empty, the default will be the current working directory [optional]

experiment_id

integer representing an experiment ID

citrus_name

character representing a new CITRUS name

citrus_id

integer representing a CITRUS ID

Details

citrus.copy_settings Copy CITRUS advanced analysis settings from an experiment and returns a CITRUS object.

citrus.delete Delete a CITRUS advanced analysis from an experiment.

citrus.download Download a CITRUS analysis from an experiment.

citrus.list List all CITRUS 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")

citrus.new Create a new CITRUS advanced analysis from an experiment and returns a CITRUS object.

citrus.rename Rename a CITRUS advanced analysis from an experiment and returns a CITRUS object.

citrus.run Run a CITRUS advanced analysis from an experiment.

citrus.show Show CITRUS advanced analysis details from an experiment and returns a CITRUS object.

citrus.status Show the status of a CITRUS advanced analysis from an experiment.

citrus.update Update a CITRUS advanced analysis from an experiment and returns the new CITRUS 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_citrus refers to a CITRUS object that is created from CITRUS endpoints
#   examples: citrus.new, citrus.show (see details section for more)

## End(Not run)
## Not run: citrus.copy_settings(cyto_session, citrus=cyto_citrus)

## Not run: citrus.delete(cyto_session, citrus=cyto_citrus)

## Not run: # Download a CITRUS analysis to the current working directory
citrus.download(cyto_session, citrus)

# Download a CITRUS analysis to a new directory
citrus.download(cyto_session, citrus, directory="/my/new/download/directory/")

## End(Not run)
## Not run: # Dataframe of all CITRUS advanced analyses with all fields present
citrus.list(cyto_session, 22)

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

## End(Not run)
## Not run: citrus.new(cyto_session, 22, citrus_name="My new CITRUS analysis")

## Not run: citrus.rename(cyto_session, citrus=cyto_citrus, citrus_name="My updated CITRUS name")

## Not run: citrus.run(cyto_session, citrus=cyto_citrus)

## Not run: citrus.show(cyto_session, 22, citrus_id=2)

## Not run: citrus.status(cyto_session, citrus=cyto_citrus)

## Not run: citrus.update(cyto_session, citrus=cyto_citrus)