CytobankAPI (version 2.2.0)

spade: SPADE Endpoints

Description

Interact with SPADE advanced analyses using these endpoints.

Usage

# S4 method for UserSession,SPADE
spade.bubbles_export(
  UserSession,
  spade,
  bubbles,
  output = "default",
  timeout = UserSession@long_timeout
)
# S4 method for UserSession,SPADE
spade.bubbles_set(
  UserSession,
  spade,
  bubbles,
  output = "default",
  timeout = UserSession@long_timeout
)
# S4 method for UserSession,SPADE
spade.bubbles_show(
  UserSession,
  spade,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession,SPADE
spade.copy_results(
  UserSession,
  spade,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession,SPADE
spade.copy_settings(
  UserSession,
  spade,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession,SPADE
spade.delete(UserSession, spade, timeout = UserSession@short_timeout)
# S4 method for UserSession,SPADE
spade.download_all(
  UserSession,
  spade,
  directory = getwd(),
  timeout = UserSession@long_timeout
)
# S4 method for UserSession,SPADE
spade.download_clusters_table(
  UserSession,
  spade,
  directory = getwd(),
  timeout = UserSession@long_timeout
)
# S4 method for UserSession,SPADE
spade.download_global_boundaries_table(
  UserSession,
  spade,
  directory = getwd(),
  timeout = UserSession@long_timeout
)
# S4 method for UserSession,SPADE
spade.download_gml(
  UserSession,
  spade,
  directory = getwd(),
  timeout = UserSession@long_timeout
)
# S4 method for UserSession,SPADE
spade.download_layout_table(
  UserSession,
  spade,
  directory = getwd(),
  timeout = UserSession@long_timeout
)
# S4 method for UserSession,SPADE
spade.download_statistics_tables(
  UserSession,
  spade,
  directory = getwd(),
  timeout = UserSession@long_timeout
)
# S4 method for UserSession
spade.list(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
spade.new(
  UserSession,
  experiment_id,
  spade_name,
  timeout = UserSession@long_timeout
)
# S4 method for UserSession,SPADE
spade.rename(
  UserSession,
  spade,
  spade_name,
  timeout = UserSession@short_timeout
)
# S4 method for UserSession,SPADE
spade.run(
  UserSession,
  spade,
  output = "default",
  timeout = UserSession@long_timeout
)
# S4 method for UserSession
spade.show(
  UserSession,
  experiment_id,
  spade_id,
  timeout = UserSession@short_timeout
)
# S4 method for UserSession,SPADE
spade.status(
  UserSession,
  spade,
  output = "default",
  timeout = UserSession@long_timeout
)
# S4 method for UserSession,SPADE
spade.update(UserSession, spade, timeout = UserSession@long_timeout)

Arguments

UserSession

Cytobank UserSession object

spade

Cytobank SPADE object

bubbles

vector/list of characters representing bubbles within a SPADE analysis, learn more about SPADE bubbles

output

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

timeout

integer representing the request timeout time in seconds [optional]

directory

character representing a specific directory (optional ending directory slash), default will be current working directory [optional]

experiment_id

integer representing an experiment ID

spade_name

character representing a new SPADE name

spade_id

integer representing a SPADE ID

Details

spade.bubbles_export Export SPADE advanced analysis bubbles from an experiment to a new experiment.

spade.bubbles_set Set SPADE advanced analysis bubbles from an experiment.

spade.bubbles_show Show SPADE advanced analysis bubbles from an experiment.

spade.copy_results Copy SPADE advanced analysis results from an experiment to a new experiment.

spade.copy_settings Copy SPADE advanced analysis settings from an experiment.

spade.delete Delete a SPADE advanced analysis from an experiment.

spade.download_all Download a SPADE advanced analysis with all data included from an experiment.

spade.download_clusters_table Download a SPADE advanced analysis global clusters table from an experiment.

spade.download_global_boundaries_table Download a SPADE advanced analysis global boundaries table from an experiment.

spade.download_gml Download a SPADE advanced analysis GML from an experiment.

spade.download_layout_table Download a SPADE advanced analysis layout table from an experiment.

spade.download_statistics_tables Download a SPADE advanced analysis statistics table from an experiment.

spade.list List all SPADE 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")

spade.new Create a new SPADE advanced analysis from an experiment and returns a SPADE object.

spade.rename Rename a SPADE advanced analysis from an experiment and returns a SPADE object.

spade.run Run a SPADE advanced analysis from an experiment.

spade.show Show SPADE advanced analysis details from an experiment and returns a SPADE object.

spade.status Show the status of a SPADE advanced analysis from an experiment.

spade.update Update a SPADE advanced analysis from an experiment and returns the new SPADE object.

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")

# cyto_spade refers to a SPADE object that is created from SPADE endpoints
#   examples: spade.new, spade.show (see details section for more)

if (FALSE) spade.bubbles_export(cyto_session, spade=cyto_spade, bubbles=c("bubble1", "bubble2"))

if (FALSE) named_bubble_list_of_node_vectors <- list("bubble_1"=c(1,2,4), "bubble_2"=8, "bubble_4"=c(10,12))
spade.bubbles_set(cyto_session, spade=cyto_spade, bubbles=named_bubble_list_of_node_vectors)

if (FALSE) spade.bubbles_show(cyto_session, spade=cyto_spade)

if (FALSE) spade.copy_results(cyto_session, spade=cyto_spade)

if (FALSE) spade.copy_settings(cyto_session, spade=cyto_spade)

if (FALSE) spade.delete(cyto_session, spade=cyto_spade)

if (FALSE) spade.download_all(cyto_session, spade=cyto_spade,
    directory="/my/new/download/directory/")

if (FALSE) spade.download_clusters_table(cyto_session, spade=cyto_spade,
  directory="/my/new/download/directory/")

if (FALSE) spade.download_global_boundaries_table(cyto_session,
  spade=cyto_spade, directory="/my/new/download/directory/")

if (FALSE) spade.download_gml(cyto_session, spade=cyto_spade,
    directory="/my/new/download/directory/")

if (FALSE) spade.download_layout_table(cyto_session, spade=cyto_spade,
    directory="/my/new/download/directory/")

if (FALSE) spade.download_statistics_tables(cyto_session, spade=cyto_spade,
  directory="/my/new/download/directory/")

if (FALSE) # Dataframe of all SPADE advanced analyses with all fields present
spade.list(cyto_session, 22)

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

if (FALSE) spade.new(cyto_session, 22, spade_name="My new SPADE analysis")

if (FALSE) spade.rename(cyto_session, spade=cyto_spade, spade_name="My updated SPADE name")

if (FALSE) spade.run(cyto_session, spade=cyto_spade)

if (FALSE) spade.show(cyto_session, 22, spade_id=2)

if (FALSE) spade.status(cyto_session, spade=cyto_spade)

if (FALSE) spade.update(cyto_session, spade=cyto_spade)