experiments: Experiment Endpoints

Description

Interact with experiment endpoints. An Experiment is a container for data and analyses in Cytobank. If data are on Cytobank, they must be within an Experiment. Configurations such as gates, compensations, scales, Sample Tags, and illustrations are also linked to an individual Experiment. Within the Cytobank interface, the Experiment Summary Page is a useful integration point for information about an Experiment.

Usage

# S4 method for UserSession
experiments.clone_full(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@long_timeout
)
# S4 method for UserSession
experiments.clone_selective(
  UserSession,
  experiment_id,
  experiment_name,
  fcs_files = c(-1),
  primary_researcher = NA,
  principal_investigator = NA,
  clone_gates = FALSE,
  clone_annotations = FALSE,
  clone_attachments = FALSE,
  clone_reagents = FALSE,
  clone_compensations = FALSE,
  clone_panels = FALSE,
  clone_illustrations = FALSE,
  clone_project = FALSE,
  clone_user_access = FALSE,
  allow_full_access_pi = FALSE,
  output = "default",
  timeout = UserSession@long_timeout
)
# S4 method for UserSession
experiments.delete(
  UserSession,
  experiment_id,
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
experiments.full_access_users_list(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
experiments.full_access_users_add(
  UserSession,
  experiment_id,
  user_id = NA,
  user_email = NA,
  username = NA,
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
experiments.full_access_users_remove(
  UserSession,
  experiment_id,
  user_id = NA,
  user_email = NA,
  username = NA,
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
experiments.list(
  UserSession,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
experiments.new(
  UserSession,
  experiment_name,
  purpose,
  comments = NA,
  primary_researcher = NA,
  principal_investigator = NA,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
experiments.show(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
experiments.trash(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
experiments.update(
  UserSession,
  experiment,
  output = "default",
  timeout = UserSession@short_timeout
)

Arguments

UserSession: Cytobank UserSession object
experiment_id: integer representing an experiment ID
output: character representing the output format [optional]
- experiments.clone_full, experiments.clone_selective, experiments.full_access_users_list, experiments.list, experiments.new, experiments.show, experiments.trash, experiments.update : ("default", "raw")
timeout: integer representing the request timeout time in seconds [optional]
experiment_name: character representing an experiment name
fcs_files: vector/list of integers representing a list of FCS file IDs [optional]
primary_researcher: integer representing a primary researcher ID [optional]
principal_investigator: integer representing a principal investigator ID [optional]
clone_gates: boolean denoting cloning gates option [optional]
clone_annotations: boolean denoting cloning annotations option [optional]
clone_attachments: boolean denoting cloning attachments option [optional]
clone_reagents: boolean denoting cloning reagents option [optional]
clone_compensations: boolean denoting cloning compensations option [optional]
clone_panels: boolean denoting cloning panels option [optional]
clone_illustrations: boolean denoting cloning illustrations option [optional]
clone_project: boolean denoting cloning project option [optional]
clone_user_access: boolean denoting cloning user access option [optional]
allow_full_access_pi: boolean denoting to allow full access to PI option [optional]
user_id: integer representing a user's ID
user_email: character representing a user's email
username: character representing a username
purpose: character representing an experiment purpose
comments: character representing an experiment comment [optional]
experiment: dataframe representing an experiment

Details

experiments.clone_full Full clone an experiment. Learn more about the full clone functionality.
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.clone_selective Selectively clone an experiment. Learn more about the selective clone functionality
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.delete Permanently delete an experiment and all analyses (including SPADE, viSNE, etc.) permanently. This is not reversible.

experiments.list List all full access users from an experiment.
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.list Add a full access user to an experiment. A full access user can be added by a user ID, email, or username.

experiments.list Remove a full access user from an experiment. A full access user can be removed by a user ID, email, or username.

experiments.list List all inbox experiments. Outputs a data frame [default] or raw list with all fields present.
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.new Create a new experiment.
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.show Show experiment details.
- Optional output parameter, specify one of the following: ("default", "raw")

experiments.trash Trash an experiment. This is reversible and not to be confused with permanent deletion.

experiments.update Update an experiment. (all parameters are optional, except for experiment_id)
- Optional output parameter, specify one of the following: ("default", "raw")

Examples

Run this code

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) experiments.clone_full(cyto_session, 22)

if (FALSE) experiments.clone_selective(cyto_session, 22,
  experiment_name="My New Experiment Name", fcs_files=c(12, 13, 14, 15, 16))

if (FALSE) experiments.delete(cyto_session, 22)

if (FALSE) # Dataframe of all full access users
experiments.full_access_users_list(cyto_session, 22)

# List of all full access users
experiments.full_access_users_list(cyto_session, 22, output="raw")

if (FALSE) # Add a user as a full access user by user's ID
experiments.full_access_users_add(cyto_session, 22, user_id=2)

# Add a user as a full access user by user's email
experiments.full_access_users_add(cyto_session, 22, user_email="sammy_cytometry@cytobank.org")

# Add a user as a full access user by user's username
experiments.full_access_users_add(cyto_session, 22, username="sammy_cytometry")

if (FALSE) # Remove a user as a full access user by user's ID
experiments.full_access_users_remove(cyto_session, 22, user_id=2)

# Remove a user as a full access user by user's email
experiments.full_access_users_remove(cyto_session, 22, user_email="sammy_cytometry@cytobank.org")

# Remove a user as a full access user by user's username
experiments.full_access_users_remove(cyto_session, 22, username="sammy_cytometry")

if (FALSE) # Dataframe of all inbox experiments with all fields present
experiments.list(cyto_session)

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

if (FALSE) experiments.new(cyto_session, "My New Experiment Name", "My experiment purpose",
  "An optional comment")

if (FALSE) experiments.show(cyto_session, 22)

if (FALSE) experiments.trash(cyto_session, 22)

if (FALSE) experiments.update(cyto_session, experiment=cyto_experiment)

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