CytobankAPI (version 2.2.0)

fcs_files: FCS File Endpoints

Description

Interact with FCS file endpoints.

Usage

# S4 method for UserSession
fcs_files.download(
  UserSession,
  experiment_id,
  fcs_file_id,
  directory = getwd(),
  timeout = UserSession@long_timeout
)
# S4 method for UserSession
fcs_files.download_zip(
  UserSession,
  experiment_id,
  fcs_files,
  timeout = UserSession@long_timeout
)
# S4 method for UserSession
fcs_files.file_internal_comp_show(
  UserSession,
  experiment_id,
  fcs_file_id,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
fcs_files.list(
  UserSession,
  experiment_id,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
fcs_files.show(
  UserSession,
  experiment_id,
  fcs_file_id,
  output = "default",
  timeout = UserSession@short_timeout
)
# S4 method for UserSession
fcs_files.upload(
  UserSession,
  experiment_id,
  file_path,
  output = "default",
  timeout = UserSession@long_timeout
)
# S4 method for UserSession
fcs_files.upload_zip(
  UserSession,
  experiment_id,
  file_path,
  output = "default",
  timeout = UserSession@long_timeout
)
# S4 method for UserSession
fcs_files.status(
  UserSession,
  experiment_id,
  timeout = UserSession@long_timeout
)

Arguments

UserSession

Cytobank UserSession object

experiment_id

integer representing an experiment ID

fcs_file_id

integer representing an FCS file ID

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]

timeout

integer representing the request timeout time in seconds [optional]

fcs_files

vector/list of integers representing a list of FCS file IDs

output

character representing the output format [optional]
- fcs_files.file_internal_comp_show : ("default", "dataframe", "raw")
- fcs_files.list, fcs_files.show, fcs_files.upload, fcs_files.upload_zip : ("default", "raw")
- dataframe: converts the file internal compensation matrix output to a dataframe

file_path

character representing a file path

Details

fcs_files.download Download an FCS file from an experiment.

fcs_files.download_zip Download all or a select set of FCS files as a zip file from an experiment. The download link of the zip file will be sent to the user's registered email address.

fcs_files.file_internal_comp_show Show FCS file internal compensation (aka spillover matrix, spill matrix, spill string) details from an experiment.
- Optional output parameter, specify one of the following: ("default", "dataframe", "raw")

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

fcs_files.show Show FCS file details from an experiment. - Optional output parameter, specify one of the following: ("default", "raw")

fcs_files.upload Upload an FCS file to an experiment. Cytobank User ID has to be attached to the UserSession object. See the help document of authenticate function for details. - Optional output parameter, specify one of the following: ("default", "raw")

fcs_files.upload_zip Upload a zip of FCS file(s) to an experiment. - Optional output parameter, specify one of the following: ("default", "raw")

fcs_files.status Check status of file(s) in an experiment. Return FALSE and print out an warming message if it fail. Otherwise, return a R dataframe object with file status information.

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) # Download an FCS file to the current working directory
fcs_files.download(cyto_session, experiment_id = 22, fcs_file_id = 4)

# Download an FCS file to a new directory
fcs_files.download(cyto_session, 22, experiment_id = 22, fcs_file_id = 4,
directory="/my/new/download/directory/")

if (FALSE) # Download all FCS files as a zip file
fcs_files.download_zip(cyto_session, experiment_id=22)

# Download a select set of FCS files as a zip file
fcs_files.download_zip(cyto_session, experiment_id=22, fcs_files=c(22, 23, 24, 25))

if (FALSE) # List of a file internal compensation, containing a file internal compensation matrix
fcs_files.file_internal_comp_show(cyto_session, 22, fcs_file_id=2)

# Dataframe only of a file internal compensation
fcs_files.file_internal_comp_show(cyto_session, 22, fcs_file_id=2, output="dataframe")

# Raw list of a file internal compensation
fcs_files.file_internal_comp_show(cyto_session, 22, fcs_file_id=2, output="raw")

if (FALSE) # Dataframe of all FCS files with all fields present
fcs_files.list(cyto_session, 22)

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

if (FALSE) fcs_files.show(cyto_session, 22, fcs_file_id=2)

if (FALSE) fcs_files.upload(cyto_session, 22, file_path="/path/to/my_fcs_file.fcs")

if (FALSE) fcs_files.upload_zip(cyto_session, 22, file_path="/path/to/my_fcs_files.zip")

if (FALSE) fcs_files.status(cyto_session, 22)