Nothing
R/flowsom.R
In CytobankAPI: Cytobank API Wrapper for R
Defines functions
create_flowsom_object
# Copyright 2020 Beckman Coulter, Inc.
# This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.
#' FlowSOM Endpoints
#'
#' Interact with FlowSOM advanced analyses using these endpoints.
#' @name flowsom
#' @param flowsom Cytobank FlowSOM object
#' @param flowsom_id integer representing a FlowSOM ID
#' @param flowsom_name character representing a new FlowSOM name
#' @param 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 \strong{[optional]}
#' @param experiment_id integer representing an \link[=experiments]{experiment} ID
#' @param output character representing the output format \strong{[optional]}\cr
#' \emph{- flowsom.list, flowsom.run, flowsom.status : \code{("default", "raw")}}
#' @param timeout integer representing the request timeout time in seconds \strong{[optional]}
#' @param UserSession Cytobank UserSession object
#' @examples \dontrun{# 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)
#' }
NULL
######################
# FlowSOM class methods
######################
setGeneric("flowsom.copy_settings", function(UserSession, flowsom, output="default", timeout=UserSession@short_timeout)
{
output_check(output, "FlowSOM", possible_outputs=c("raw"))
standardGeneric("flowsom.copy_settings")
})
#' @rdname flowsom
#' @aliases flowsom.copy_settings
#'
#' @details \code{flowsom.copy_settings} Copy FlowSOM advanced analysis settings from an experiment and returns a FlowSOM object.
#' @examples \dontrun{flowsom.copy_settings(cyto_session, flowsom=cyto_flowsom)
#' }
#' @export
setMethod("flowsom.copy_settings", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, output="default", timeout=UserSession@short_timeout)
{
resp <- POST(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, "/copy_settings", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
if (output == "default")
{
return(cyto_dataframe(parse(resp, "FlowSOM")))
}
else # if (output == "raw")
{
return(parse(resp, "FlowSOM"))
}
})
setGeneric("flowsom.delete", function(UserSession, flowsom, timeout=UserSession@short_timeout)
{
standardGeneric("flowsom.delete")
})
#' @rdname flowsom
#' @aliases flowsom.delete
#'
#' @details \code{flowsom.delete} Delete a FlowSOM advanced analysis from an experiment.
#' @examples \dontrun{flowsom.delete(cyto_session, flowsom=cyto_flowsom)
#' }
#' @export
setMethod("flowsom.delete", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, timeout=UserSession@short_timeout)
{
resp <- DELETE(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
if (http_error(resp))
{
error_parse(resp, "experiments")
}
return(paste("FlowSOM (ID=", flowsom@flowsom_id, ") successfully deleted.", sep=""))
})
setGeneric("flowsom.download", function(UserSession, flowsom, directory=getwd(), timeout=UserSession@long_timeout)
{
standardGeneric("flowsom.download")
})
#' @rdname flowsom
#' @aliases flowsom.download
#'
#' @details \code{flowsom.download} Download a FlowSOM analysis from an experiment.
#' @examples \dontrun{# 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/")
#' }
#' @export
setMethod("flowsom.download", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, directory=getwd(), timeout=UserSession@long_timeout)
{
if (is.na(flowsom@attachment_id))
{
stop(
sprintf(
paste("Cytobank API 'FlowSOM' request failed [client]\n Must provide a valid FlowSOM attachment ID, cannot be NA", sep="")
),
call. = FALSE
)
}
temp_directory <- directory_file_join(directory, "tmp.part")
baseURL = get_base_url(UserSession)
fs_info <- attachments.show(UserSession, flowsom@created_experiment, flowsom@attachment_id)
file_hashkey <- unlist(fs_info$uniqueHash)
file_name <- unlist(fs_info$filename)
file_type <- sub('.*\\.', '', file_name)
resp <- GET(paste(baseURL,'/download/url?', "experimentId=", flowsom@created_experiment, "&hashKey=", file_hashkey,
"&fileName=", utils::URLencode(file_name),
"&fileType=",determine_file_type(file_type), sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token))
)
download_status<-utils::download.file(url=parse(resp)$downloadUrl,
destfile=file.path(directory,file_name),
method = 'auto', quiet = FALSE, mode = 'wb')
if(download_status!=0){
print('Can not download the file.')
return(FALSE)
}else{
print(paste('File has been downloaded and saved to: ',file.path(directory,file_name),sep=""))
return(TRUE)
}
if (http_error(resp))
{
error_parse(resp, "flowsom")
}
return(rename_temp_file(resp, directory))
})
setGeneric("flowsom.list", function(UserSession, experiment_id, output="default", timeout=UserSession@short_timeout)
{
standardGeneric("flowsom.list")
})
#' @rdname flowsom
#' @aliases flowsom.list
#'
#' @details \code{flowsom.list} List all FlowSOM advanced analyses from an experiment. Outputs a dataframe [default] or list with all fields present.\cr
#' \emph{- Optional output parameter, specify one of the following: \code{("default", "raw")}}
#' @examples \dontrun{# Dataframe of all FlowSOM advanced analyses with all fields present
#' flowsom.list(cyto_session, 22)
#'
#' # Raw list of all FlowSOM advanced analyses with all fields present
#' flowsom.list(cyto_session, 22, output="raw")
#' }
#' @export
setMethod("flowsom.list", signature(UserSession="UserSession"), function(UserSession, experiment_id, output="default", timeout=UserSession@short_timeout)
{
output_check(output, "FlowSOM", possible_outputs=c("raw"))
resp <- GET(paste(UserSession@site, "/experiments/", experiment_id, "/advanced_analyses/flowsom", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
if (output == "default")
{
return(cyto_dataframe(parse(resp, "FlowSOM")$flowsom))
}
else # if (output == "raw")
{
return(parse(resp, "FlowSOM"))
}
})
setGeneric("flowsom.new", function(UserSession, experiment_id, flowsom_name, timeout=UserSession@long_timeout)
{
standardGeneric("flowsom.new")
})
#' @rdname flowsom
#' @aliases flowsom.new
#'
#' @details \code{flowsom.new} Create a new FlowSOM advanced analysis from an experiment and returns a FlowSOM object.
#' @examples \dontrun{flowsom.new(cyto_session, 22, flowsom_name="My new FlowSOM analysis")
#' }
#' @export
setMethod("flowsom.new", signature(UserSession="UserSession"), function(UserSession, experiment_id, flowsom_name, timeout=UserSession@long_timeout)
{
resp <- POST(paste(UserSession@site, "/experiments/", experiment_id, "/advanced_analyses/flowsom/", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
body=list(name=flowsom_name),
encode="json",
timeout(timeout)
)
return(create_flowsom_object(UserSession, parse(resp, "FlowSOM")))
})
setGeneric("flowsom.rename", function(UserSession, flowsom, flowsom_name, timeout=UserSession@short_timeout)
{
standardGeneric("flowsom.rename")
})
#' @rdname flowsom
#' @aliases flowsom.rename
#'
#' @details \code{flowsom.rename} Rename a FlowSOM advanced analysis from an experiment and returns a FlowSOM object.
#' @examples \dontrun{flowsom.rename(cyto_session, flowsom=cyto_flowsom,
#' flowsom_name="My updated FlowSOM name")
#' }
#' @export
setMethod("flowsom.rename", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, flowsom_name, timeout=UserSession@short_timeout)
{
resp <- PUT(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, "/rename", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
body=list(name=flowsom_name),
encode="json",
timeout(timeout)
)
flowsom@name <- parse(resp, "FlowSOM")$flowsom$name
return(flowsom)
})
setGeneric("flowsom.run", function(UserSession, flowsom, output="default", timeout=UserSession@long_timeout)
{
standardGeneric("flowsom.run")
})
#' @rdname flowsom
#' @aliases flowsom.run
#'
#' @details \code{flowsom.run} Run a FlowSOM advanced analysis from an experiment.
#' @examples \dontrun{flowsom.run(cyto_session, flowsom=cyto_flowsom)
#' }
#' @export
setMethod("flowsom.run", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, output="default", timeout=UserSession@long_timeout)
{
output_check(output, "FlowSOM", possible_outputs=c("raw"))
resp <- POST(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, "/run", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
if (output == "default")
{
return(cyto_dataframe(parse(resp, "FlowSOM")))
}
else # if (output == "raw")
{
return(parse(resp, "FlowSOM"))
}
})
setGeneric("flowsom.show", function(UserSession, experiment_id, flowsom_id, timeout=UserSession@short_timeout)
{
standardGeneric("flowsom.show")
})
#' @rdname flowsom
#' @aliases flowsom.show
#'
#' @details \code{flowsom.show} Show FlowSOM advanced analysis details from an experiment and returns a FlowSOM object.
#' @examples \dontrun{flowsom.show(cyto_session, 22, flowsom_id=2)
#' }
#' @export
setMethod("flowsom.show", signature(UserSession="UserSession"), function(UserSession, experiment_id, flowsom_id, timeout=UserSession@short_timeout)
{
resp <- GET(paste(UserSession@site, "/experiments/", experiment_id, "/advanced_analyses/flowsom/", flowsom_id, "?include_settings=1", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
return(create_flowsom_object(UserSession, parse(resp, "FlowSOM")))
})
setGeneric("flowsom.status", function(UserSession, flowsom, output="default", timeout=UserSession@long_timeout)
{
standardGeneric("flowsom.status")
})
#' @rdname flowsom
#' @aliases flowsom.status
#'
#' @details \code{flowsom.status} Show the status of a FlowSOM advanced analysis from an experiment.
#' @examples \dontrun{flowsom.status(cyto_session, flowsom=cyto_flowsom)
#' }
#' @export
setMethod("flowsom.status", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, output="default", timeout=UserSession@long_timeout)
{
output_check(output, "FlowSOM", possible_outputs=c("raw"))
resp <- GET(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, "/status", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
if (output == "default")
{
return(cyto_dataframe(parse(resp, "FlowSOM")))
}
else # if (output == "raw")
{
return(parse(resp, "FlowSOM"))
}
})
setGeneric("flowsom.update", function(UserSession, flowsom, timeout=UserSession@long_timeout)
{
standardGeneric("flowsom.update")
})
#' @rdname flowsom
#' @aliases flowsom.update
#'
#' @details \code{flowsom.update} Update a FlowSOM advanced analysis from an experiment and returns the new FlowSOM object.
#' @examples \dontrun{flowsom.update(cyto_session, flowsom=cyto_flowsom)
#' }
#' @export
setMethod("flowsom.update", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, timeout=UserSession@long_timeout)
{
if (length(flowsom@channels) && is.character(flowsom@channels[[1]]))
{
flowsom@channels <- as.list(helper.channel_ids_from_long_names(flowsom@.available_channels, flowsom@channels))
if (!length(flowsom@channels_to_plot))
{
flowsom@channels_to_plot <- flowsom@channels
}
}
if (length(flowsom@channels_to_plot) && is.character(flowsom@channels_to_plot[[1]]))
{
flowsom@channels_to_plot <- as.list(helper.channel_ids_from_long_names(flowsom@.available_channels, flowsom@channels_to_plot))
}
# required settings for running FlowSOM
if (!length(flowsom@fcs_files))
{
stop(
sprintf (
"Cytobank API 'flowsom.update' request failed [client]\n Must specify FCS file IDs in order to update."
),
call. = FALSE
)
}
if (!length(flowsom@channels))
{
stop(
sprintf (
"Cytobank API 'flowsom.update' request failed [client]\n Must specify clustering channels in order to update."
),
call. = FALSE
)
}
resp <- PUT(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
body=list(options=list(
clusteringChannels=flowsom@channels,
clusteringMethod=flowsom@clustering_method,
compensationId=flowsom@compensation_id,
desiredEventsPerFile=flowsom@desired_events_per_file,
desiredTotalEvents=flowsom@desired_total_events,
eventSamplingMethod=flowsom@event_sampling_method,
expectedClusters=flowsom@expected_clusters,
expectedMetaclusters=flowsom@expected_metaclusters,
fcsFileIds=flowsom@fcs_files,
gateSetId=flowsom@population_id,
iterations=flowsom@iterations,
normalizeScales=flowsom@normalize_scales,
randomSeed=flowsom@random_seed,
SOMCreationMethod=flowsom@som_creation_method,
externalSOMAnalysisId=flowsom@external_som_analysis_id,
channelsToPlot=flowsom@channels_to_plot,
clusterSizeType=flowsom@cluster_size_type,
fixedClusterSize=flowsom@fixed_cluster_size,
gateSetNamesToLabe=flowsom@gate_set_names_to_label,
maxRelativeClusterSize=flowsom@max_relative_cluster_size,
outputFileType=flowsom@output_file_type,
showBackgroundOnLegend=flowsom@show_background_on_legend,
showBackgroundOnChannelColoredMSTs=flowsom@show_background_on_channel_colored_msts,
showBackgroundOnPopulationPies=flowsom@show_background_on_population_pies
)
),
encode="json",
timeout(timeout)
)
return(create_flowsom_object(UserSession, parse(resp, "FlowSOM")))
})
##########################
# FlowSOM HELPER FUNCTIONS
##########################
##########
# PRIVATE
##########
# Create FlowSOM object from FlowSOM json response
create_flowsom_object <- function(UserSession, flowsom_response)
{
fcs_files <- fcs_files.list(UserSession, flowsom_response$flowsom$sourceExperiment)
return(
new("FlowSOM",
attachment_id=if (!is.integer(flowsom_response$flowsom$settings$attachmentId)) NA_integer_ else flowsom_response$flowsom$settings$attachmentId,
author=flowsom_response$flowsom$author,
auto_seed=if (!is.logical(flowsom_response$flowsom$settings$random_seed)) TRUE else flowsom_response$flowsom$settings$autoSeed,
canceled=flowsom_response$flowsom$canceled,
channels=flowsom_response$flowsom$settings$clusteringChannels,
channels_to_plot=flowsom_response$flowsom$settings$channelsToPlot,
clustering_method=flowsom_response$flowsom$settings$clusteringMethod,
cluster_size_type=flowsom_response$flowsom$settings$clusterSizeType,
completed=flowsom_response$flowsom$completed,
compensation_id=flowsom_response$flowsom$settings$compensationId,
created_experiment=if (!is.integer(flowsom_response$flowsom$createdExperiment)) NA_integer_ else flowsom_response$flowsom$createdExperiment,
desired_events_per_file=flowsom_response$flowsom$settings$desiredEventsPerFile,
desired_total_events=flowsom_response$flowsom$settings$desiredTotalEvents,
event_sampling_method=flowsom_response$flowsom$settings$eventSamplingMethod,
expected_clusters=flowsom_response$flowsom$settings$expectedClusters,
expected_metaclusters=flowsom_response$flowsom$settings$expectedMetaclusters,
external_som_analysis_info=flowsom_response$flowsom$settings$externalSOMAnalysisInfo,
external_som_analysis_id=flowsom_response$flowsom$settings$externalSOMAnalysisId,
fcs_files=flowsom_response$flowsom$settings$fcsFileIds,
final_result=flowsom_response$flowsom$settings$finalResult,
fixed_cluster_size=flowsom_response$flowsom$settings$fixedClusterSize,
flowsom_id=flowsom_response$flowsom$id,
gate_set_names_to_label=flowsom_response$flowsom$settings$gateSetNamesToLabel,
iterations=flowsom_response$flowsom$settings$iterations,
max_relative_cluster_size=flowsom_response$flowsom$settings$maxRelativeClusterSize,
name=flowsom_response$flowsom$name,
normalize_scales=flowsom_response$flowsom$settings$normalizeScales,
num_events_to_actually_sample=if (!is.integer(flowsom_response$flowsom$settings$numEventsToActuallySample)) 0 else flowsom_response$flowsom$settings$numEventsToActuallySample,
num_fcs_files=if (!is.integer(flowsom_response$flowsom$settings$numFcsFiles)) 0 else flowsom_response$flowsom$settings$numFcsFiles,
output_file_type=flowsom_response$flowsom$settings$outputFileType,
population_id=flowsom_response$flowsom$settings$gateSetId,
random_seed=if (!is.integer(flowsom_response$flowsom$settings$randomSeed)) NA_integer_ else flowsom_response$flowsom$settings$randomSeed,
show_background_on_legend=flowsom_response$flowsom$settings$showBackgroundOnLegend,
show_background_on_channel_colored_msts=flowsom_response$flowsom$settings$showBackgroundOnChannelColoredMSTs,
show_background_on_population_pies=flowsom_response$flowsom$settings$showBackgroundOnPopulationPies,
som_creation_method=flowsom_response$flowsom$settings$SOMCreationMethod,
source_experiment=flowsom_response$flowsom$sourceExperiment,
status=flowsom_response$flowsom$status,
type=flowsom_response$flowsom$type,
.available_channels=panels.list(UserSession, flowsom_response$flowsom$sourceExperiment),
.available_files=fcs_files,
.available_populations=populations.list(UserSession, flowsom_response$flowsom$sourceExperiment))
)
}
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Defines functions create_flowsom_object
# Copyright 2020 Beckman Coulter, Inc.
# This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.
#' FlowSOM Endpoints
#'
#' Interact with FlowSOM advanced analyses using these endpoints.
#' @name flowsom
#' @param flowsom Cytobank FlowSOM object
#' @param flowsom_id integer representing a FlowSOM ID
#' @param flowsom_name character representing a new FlowSOM name
#' @param 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 \strong{[optional]}
#' @param experiment_id integer representing an \link[=experiments]{experiment} ID
#' @param output character representing the output format \strong{[optional]}\cr
#' \emph{- flowsom.list, flowsom.run, flowsom.status : \code{("default", "raw")}}
#' @param timeout integer representing the request timeout time in seconds \strong{[optional]}
#' @param UserSession Cytobank UserSession object
#' @examples \dontrun{# 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)
#' }
NULL
######################
# FlowSOM class methods
######################
setGeneric("flowsom.copy_settings", function(UserSession, flowsom, output="default", timeout=UserSession@short_timeout)
{
output_check(output, "FlowSOM", possible_outputs=c("raw"))
standardGeneric("flowsom.copy_settings")
})
#' @rdname flowsom
#' @aliases flowsom.copy_settings
#'
#' @details \code{flowsom.copy_settings} Copy FlowSOM advanced analysis settings from an experiment and returns a FlowSOM object.
#' @examples \dontrun{flowsom.copy_settings(cyto_session, flowsom=cyto_flowsom)
#' }
#' @export
setMethod("flowsom.copy_settings", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, output="default", timeout=UserSession@short_timeout)
{
resp <- POST(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, "/copy_settings", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
if (output == "default")
{
return(cyto_dataframe(parse(resp, "FlowSOM")))
}
else # if (output == "raw")
{
return(parse(resp, "FlowSOM"))
}
})
setGeneric("flowsom.delete", function(UserSession, flowsom, timeout=UserSession@short_timeout)
{
standardGeneric("flowsom.delete")
})
#' @rdname flowsom
#' @aliases flowsom.delete
#'
#' @details \code{flowsom.delete} Delete a FlowSOM advanced analysis from an experiment.
#' @examples \dontrun{flowsom.delete(cyto_session, flowsom=cyto_flowsom)
#' }
#' @export
setMethod("flowsom.delete", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, timeout=UserSession@short_timeout)
{
resp <- DELETE(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
if (http_error(resp))
{
error_parse(resp, "experiments")
}
return(paste("FlowSOM (ID=", flowsom@flowsom_id, ") successfully deleted.", sep=""))
})
setGeneric("flowsom.download", function(UserSession, flowsom, directory=getwd(), timeout=UserSession@long_timeout)
{
standardGeneric("flowsom.download")
})
#' @rdname flowsom
#' @aliases flowsom.download
#'
#' @details \code{flowsom.download} Download a FlowSOM analysis from an experiment.
#' @examples \dontrun{# 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/")
#' }
#' @export
setMethod("flowsom.download", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, directory=getwd(), timeout=UserSession@long_timeout)
{
if (is.na(flowsom@attachment_id))
{
stop(
sprintf(
paste("Cytobank API 'FlowSOM' request failed [client]\n Must provide a valid FlowSOM attachment ID, cannot be NA", sep="")
),
call. = FALSE
)
}
temp_directory <- directory_file_join(directory, "tmp.part")
baseURL = get_base_url(UserSession)
fs_info <- attachments.show(UserSession, flowsom@created_experiment, flowsom@attachment_id)
file_hashkey <- unlist(fs_info$uniqueHash)
file_name <- unlist(fs_info$filename)
file_type <- sub('.*\\.', '', file_name)
resp <- GET(paste(baseURL,'/download/url?', "experimentId=", flowsom@created_experiment, "&hashKey=", file_hashkey,
"&fileName=", utils::URLencode(file_name),
"&fileType=",determine_file_type(file_type), sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token))
)
download_status<-utils::download.file(url=parse(resp)$downloadUrl,
destfile=file.path(directory,file_name),
method = 'auto', quiet = FALSE, mode = 'wb')
if(download_status!=0){
print('Can not download the file.')
return(FALSE)
}else{
print(paste('File has been downloaded and saved to: ',file.path(directory,file_name),sep=""))
return(TRUE)
}
if (http_error(resp))
{
error_parse(resp, "flowsom")
}
return(rename_temp_file(resp, directory))
})
setGeneric("flowsom.list", function(UserSession, experiment_id, output="default", timeout=UserSession@short_timeout)
{
standardGeneric("flowsom.list")
})
#' @rdname flowsom
#' @aliases flowsom.list
#'
#' @details \code{flowsom.list} List all FlowSOM advanced analyses from an experiment. Outputs a dataframe [default] or list with all fields present.\cr
#' \emph{- Optional output parameter, specify one of the following: \code{("default", "raw")}}
#' @examples \dontrun{# 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")
#' }
#' @export
setMethod("flowsom.list", signature(UserSession="UserSession"), function(UserSession, experiment_id, output="default", timeout=UserSession@short_timeout)
{
output_check(output, "FlowSOM", possible_outputs=c("raw"))
resp <- GET(paste(UserSession@site, "/experiments/", experiment_id, "/advanced_analyses/flowsom", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
if (output == "default")
{
return(cyto_dataframe(parse(resp, "FlowSOM")$flowsom))
}
else # if (output == "raw")
{
return(parse(resp, "FlowSOM"))
}
})
setGeneric("flowsom.new", function(UserSession, experiment_id, flowsom_name, timeout=UserSession@long_timeout)
{
standardGeneric("flowsom.new")
})
#' @rdname flowsom
#' @aliases flowsom.new
#'
#' @details \code{flowsom.new} Create a new FlowSOM advanced analysis from an experiment and returns a FlowSOM object.
#' @examples \dontrun{flowsom.new(cyto_session, 22, flowsom_name="My new FlowSOM analysis")
#' }
#' @export
setMethod("flowsom.new", signature(UserSession="UserSession"), function(UserSession, experiment_id, flowsom_name, timeout=UserSession@long_timeout)
{
resp <- POST(paste(UserSession@site, "/experiments/", experiment_id, "/advanced_analyses/flowsom/", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
body=list(name=flowsom_name),
encode="json",
timeout(timeout)
)
return(create_flowsom_object(UserSession, parse(resp, "FlowSOM")))
})
setGeneric("flowsom.rename", function(UserSession, flowsom, flowsom_name, timeout=UserSession@short_timeout)
{
standardGeneric("flowsom.rename")
})
#' @rdname flowsom
#' @aliases flowsom.rename
#'
#' @details \code{flowsom.rename} Rename a FlowSOM advanced analysis from an experiment and returns a FlowSOM object.
#' @examples \dontrun{flowsom.rename(cyto_session, flowsom=cyto_flowsom,
#' flowsom_name="My updated FlowSOM name")
#' }
#' @export
setMethod("flowsom.rename", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, flowsom_name, timeout=UserSession@short_timeout)
{
resp <- PUT(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, "/rename", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
body=list(name=flowsom_name),
encode="json",
timeout(timeout)
)
flowsom@name <- parse(resp, "FlowSOM")$flowsom$name
return(flowsom)
})
setGeneric("flowsom.run", function(UserSession, flowsom, output="default", timeout=UserSession@long_timeout)
{
standardGeneric("flowsom.run")
})
#' @rdname flowsom
#' @aliases flowsom.run
#'
#' @details \code{flowsom.run} Run a FlowSOM advanced analysis from an experiment.
#' @examples \dontrun{flowsom.run(cyto_session, flowsom=cyto_flowsom)
#' }
#' @export
setMethod("flowsom.run", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, output="default", timeout=UserSession@long_timeout)
{
output_check(output, "FlowSOM", possible_outputs=c("raw"))
resp <- POST(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, "/run", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
if (output == "default")
{
return(cyto_dataframe(parse(resp, "FlowSOM")))
}
else # if (output == "raw")
{
return(parse(resp, "FlowSOM"))
}
})
setGeneric("flowsom.show", function(UserSession, experiment_id, flowsom_id, timeout=UserSession@short_timeout)
{
standardGeneric("flowsom.show")
})
#' @rdname flowsom
#' @aliases flowsom.show
#'
#' @details \code{flowsom.show} Show FlowSOM advanced analysis details from an experiment and returns a FlowSOM object.
#' @examples \dontrun{flowsom.show(cyto_session, 22, flowsom_id=2)
#' }
#' @export
setMethod("flowsom.show", signature(UserSession="UserSession"), function(UserSession, experiment_id, flowsom_id, timeout=UserSession@short_timeout)
{
resp <- GET(paste(UserSession@site, "/experiments/", experiment_id, "/advanced_analyses/flowsom/", flowsom_id, "?include_settings=1", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
return(create_flowsom_object(UserSession, parse(resp, "FlowSOM")))
})
setGeneric("flowsom.status", function(UserSession, flowsom, output="default", timeout=UserSession@long_timeout)
{
standardGeneric("flowsom.status")
})
#' @rdname flowsom
#' @aliases flowsom.status
#'
#' @details \code{flowsom.status} Show the status of a FlowSOM advanced analysis from an experiment.
#' @examples \dontrun{flowsom.status(cyto_session, flowsom=cyto_flowsom)
#' }
#' @export
setMethod("flowsom.status", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, output="default", timeout=UserSession@long_timeout)
{
output_check(output, "FlowSOM", possible_outputs=c("raw"))
resp <- GET(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, "/status", sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
timeout(timeout)
)
if (output == "default")
{
return(cyto_dataframe(parse(resp, "FlowSOM")))
}
else # if (output == "raw")
{
return(parse(resp, "FlowSOM"))
}
})
setGeneric("flowsom.update", function(UserSession, flowsom, timeout=UserSession@long_timeout)
{
standardGeneric("flowsom.update")
})
#' @rdname flowsom
#' @aliases flowsom.update
#'
#' @details \code{flowsom.update} Update a FlowSOM advanced analysis from an experiment and returns the new FlowSOM object.
#' @examples \dontrun{flowsom.update(cyto_session, flowsom=cyto_flowsom)
#' }
#' @export
setMethod("flowsom.update", signature(UserSession="UserSession", flowsom="FlowSOM"), function(UserSession, flowsom, timeout=UserSession@long_timeout)
{
if (length(flowsom@channels) && is.character(flowsom@channels[[1]]))
{
flowsom@channels <- as.list(helper.channel_ids_from_long_names(flowsom@.available_channels, flowsom@channels))
if (!length(flowsom@channels_to_plot))
{
flowsom@channels_to_plot <- flowsom@channels
}
}
if (length(flowsom@channels_to_plot) && is.character(flowsom@channels_to_plot[[1]]))
{
flowsom@channels_to_plot <- as.list(helper.channel_ids_from_long_names(flowsom@.available_channels, flowsom@channels_to_plot))
}
# required settings for running FlowSOM
if (!length(flowsom@fcs_files))
{
stop(
sprintf (
"Cytobank API 'flowsom.update' request failed [client]\n Must specify FCS file IDs in order to update."
),
call. = FALSE
)
}
if (!length(flowsom@channels))
{
stop(
sprintf (
"Cytobank API 'flowsom.update' request failed [client]\n Must specify clustering channels in order to update."
),
call. = FALSE
)
}
resp <- PUT(paste(UserSession@site, "/experiments/", flowsom@source_experiment, "/advanced_analyses/flowsom/", flowsom@flowsom_id, sep=""),
add_headers(Authorization=paste("Bearer", UserSession@auth_token)),
body=list(options=list(
clusteringChannels=flowsom@channels,
clusteringMethod=flowsom@clustering_method,
compensationId=flowsom@compensation_id,
desiredEventsPerFile=flowsom@desired_events_per_file,
desiredTotalEvents=flowsom@desired_total_events,
eventSamplingMethod=flowsom@event_sampling_method,
expectedClusters=flowsom@expected_clusters,
expectedMetaclusters=flowsom@expected_metaclusters,
fcsFileIds=flowsom@fcs_files,
gateSetId=flowsom@population_id,
iterations=flowsom@iterations,
normalizeScales=flowsom@normalize_scales,
randomSeed=flowsom@random_seed,
SOMCreationMethod=flowsom@som_creation_method,
externalSOMAnalysisId=flowsom@external_som_analysis_id,
channelsToPlot=flowsom@channels_to_plot,
clusterSizeType=flowsom@cluster_size_type,
fixedClusterSize=flowsom@fixed_cluster_size,
gateSetNamesToLabe=flowsom@gate_set_names_to_label,
maxRelativeClusterSize=flowsom@max_relative_cluster_size,
outputFileType=flowsom@output_file_type,
showBackgroundOnLegend=flowsom@show_background_on_legend,
showBackgroundOnChannelColoredMSTs=flowsom@show_background_on_channel_colored_msts,
showBackgroundOnPopulationPies=flowsom@show_background_on_population_pies
)
),
encode="json",
timeout(timeout)
)
return(create_flowsom_object(UserSession, parse(resp, "FlowSOM")))
})
##########################
# FlowSOM HELPER FUNCTIONS
##########################
##########
# PRIVATE
##########
# Create FlowSOM object from FlowSOM json response
create_flowsom_object <- function(UserSession, flowsom_response)
{
fcs_files <- fcs_files.list(UserSession, flowsom_response$flowsom$sourceExperiment)
return(
new("FlowSOM",
attachment_id=if (!is.integer(flowsom_response$flowsom$settings$attachmentId)) NA_integer_ else flowsom_response$flowsom$settings$attachmentId,
author=flowsom_response$flowsom$author,
auto_seed=if (!is.logical(flowsom_response$flowsom$settings$random_seed)) TRUE else flowsom_response$flowsom$settings$autoSeed,
canceled=flowsom_response$flowsom$canceled,
channels=flowsom_response$flowsom$settings$clusteringChannels,
channels_to_plot=flowsom_response$flowsom$settings$channelsToPlot,
clustering_method=flowsom_response$flowsom$settings$clusteringMethod,
cluster_size_type=flowsom_response$flowsom$settings$clusterSizeType,
completed=flowsom_response$flowsom$completed,
compensation_id=flowsom_response$flowsom$settings$compensationId,
created_experiment=if (!is.integer(flowsom_response$flowsom$createdExperiment)) NA_integer_ else flowsom_response$flowsom$createdExperiment,
desired_events_per_file=flowsom_response$flowsom$settings$desiredEventsPerFile,
desired_total_events=flowsom_response$flowsom$settings$desiredTotalEvents,
event_sampling_method=flowsom_response$flowsom$settings$eventSamplingMethod,
expected_clusters=flowsom_response$flowsom$settings$expectedClusters,
expected_metaclusters=flowsom_response$flowsom$settings$expectedMetaclusters,
external_som_analysis_info=flowsom_response$flowsom$settings$externalSOMAnalysisInfo,
external_som_analysis_id=flowsom_response$flowsom$settings$externalSOMAnalysisId,
fcs_files=flowsom_response$flowsom$settings$fcsFileIds,
final_result=flowsom_response$flowsom$settings$finalResult,
fixed_cluster_size=flowsom_response$flowsom$settings$fixedClusterSize,
flowsom_id=flowsom_response$flowsom$id,
gate_set_names_to_label=flowsom_response$flowsom$settings$gateSetNamesToLabel,
iterations=flowsom_response$flowsom$settings$iterations,
max_relative_cluster_size=flowsom_response$flowsom$settings$maxRelativeClusterSize,
name=flowsom_response$flowsom$name,
normalize_scales=flowsom_response$flowsom$settings$normalizeScales,
num_events_to_actually_sample=if (!is.integer(flowsom_response$flowsom$settings$numEventsToActuallySample)) 0 else flowsom_response$flowsom$settings$numEventsToActuallySample,
num_fcs_files=if (!is.integer(flowsom_response$flowsom$settings$numFcsFiles)) 0 else flowsom_response$flowsom$settings$numFcsFiles,
output_file_type=flowsom_response$flowsom$settings$outputFileType,
population_id=flowsom_response$flowsom$settings$gateSetId,
random_seed=if (!is.integer(flowsom_response$flowsom$settings$randomSeed)) NA_integer_ else flowsom_response$flowsom$settings$randomSeed,
show_background_on_legend=flowsom_response$flowsom$settings$showBackgroundOnLegend,
show_background_on_channel_colored_msts=flowsom_response$flowsom$settings$showBackgroundOnChannelColoredMSTs,
show_background_on_population_pies=flowsom_response$flowsom$settings$showBackgroundOnPopulationPies,
som_creation_method=flowsom_response$flowsom$settings$SOMCreationMethod,
source_experiment=flowsom_response$flowsom$sourceExperiment,
status=flowsom_response$flowsom$status,
type=flowsom_response$flowsom$type,
.available_channels=panels.list(UserSession, flowsom_response$flowsom$sourceExperiment),
.available_files=fcs_files,
.available_populations=populations.list(UserSession, flowsom_response$flowsom$sourceExperiment))
)
}
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