visne {CytobankAPI} | R Documentation |
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] |
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))