flowsom {CytobankAPI}

FlowSOM Endpoints

Description

Interact with FlowSOM advanced analyses using these endpoints.

Usage

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

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

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

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

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

## S4 method for signature 'UserSession,FlowSOM'
flowsom.rename(
  UserSession,
  flowsom,
  flowsom_name,
  timeout = UserSession@short_timeout
)

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

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

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

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

Arguments

UserSession

Cytobank UserSession object

flowsom

Cytobank FlowSOM object

output

character representing the output format [optional]
- flowsom.list, flowsom.run, flowsom.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

flowsom_name

character representing a new FlowSOM name

flowsom_id

integer representing a FlowSOM ID

Details

flowsom.copy_settings Copy FlowSOM advanced analysis settings from an experiment and returns a FlowSOM object.

flowsom.delete Delete a FlowSOM advanced analysis from an experiment.

flowsom.download Download a FlowSOM analysis from an experiment.

flowsom.list List all FlowSOM 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")

flowsom.new Create a new FlowSOM advanced analysis from an experiment and returns a FlowSOM object.

flowsom.rename Rename a FlowSOM advanced analysis from an experiment and returns a FlowSOM object.

flowsom.run Run a FlowSOM advanced analysis from an experiment.

flowsom.show Show FlowSOM advanced analysis details from an experiment and returns a FlowSOM object.

flowsom.status Show the status of a FlowSOM advanced analysis from an experiment.

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

## End(Not run)
## Not run: flowsom.copy_settings(cyto_session, flowsom=cyto_flowsom)

## Not run: flowsom.delete(cyto_session, flowsom=cyto_flowsom)

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

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

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

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

## End(Not run)
## Not run: flowsom.new(cyto_session, 22, flowsom_name="My new FlowSOM analysis")

## Not run: flowsom.rename(cyto_session, flowsom=cyto_flowsom,
    flowsom_name="My updated FlowSOM name")

## End(Not run)
## Not run: flowsom.run(cyto_session, flowsom=cyto_flowsom)

## Not run: flowsom.show(cyto_session, 22, flowsom_id=2)

## Not run: flowsom.status(cyto_session, flowsom=cyto_flowsom)

## Not run: flowsom.update(cyto_session, flowsom=cyto_flowsom)