CytobankAPI (version 2.2.0)

compensations: Compensation Endpoints

Description

Interact with compensation endpoints. Get information about compensations stored in Cytobank. For information about file-internal compensation for an individual FCS file, consult the FCS files endpoints. Learn more about compensation in Cytobank.

Usage

# S4 method for UserSession
compensations.upload_csv(
  UserSession,
  experiment_id,
  file_path,
  timeout = UserSession@long_timeout
)
# S4 method for UserSession
compensations.list(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
compensations.show(
  UserSession,
  experiment_id,
  compensation_id,
  output = "default",
  timeout = UserSession@short_timeout
)

Arguments

UserSession

Cytobank UserSession object

experiment_id

integer representing an experiment ID

file_path

character representing a file path

timeout

integer representing the request timeout time in seconds [optional]

output

character representing the output format [optional]
- compensations.list : ("default", "raw") - compensations.show : ("default", "dataframe", "raw") - dataframe: converts the compensation matrix output to a dataframe

compensation_id

integer representing a compensation ID

Details

compensations.upload_csv Upload a compensation CSV to an experiment.

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

compensations.show Show compensation details from an experiment.
- Optional output parameter, specify one of the following: ("default", "dataframe", "raw")
- dataframe: converts the compensation matrix output to a dataframe

Examples

if (FALSE) # 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")

if (FALSE) compensations.upload_csv(cyto_session, 22, file_path="/path/to/my_compensation.csv")

if (FALSE) # List of all compensations with all fields present, with a compensation matrix dataframe list item
compensations.list(cyto_session, 22)

# Raw list of all compensations with all fields present
compensations.list(cyto_session, 22, output="raw")

if (FALSE) # List form of a compensation
compensations.show(cyto_session, 22, compensation_id=2)

# Compensation dataframe only
compensations.show(cyto_session, 22, compensation_id=2, output="dataframe")