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R/NaviCell_RC.R
In RNaviCell: Visualization of High-Throughput Data on Large-Scale Biological Networks
# RNaviCell package
#
# Copyright (C) {2015} {Institut Curie, 26 rue d'Ulm, 75005 Paris}
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library 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
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301
# USA
#' NaviCell reference class
#'
#' NaviCell (https://navicell.curie.fr) is a web-based environment for
#' browsing, commenting and analyzing very large biological molecular networks
#' using Google Maps and for visualizing 'omics' data on top of the network
#' maps.
#'
#' NaviCell can also act as a server allowing to be remotely controlled through
#' a REST API. A python and a R language bindings have been developped on top
#' of the REST API to hide technical details and to provide users and
#' programmers a friendly interface. A Java binding has been initiated.
#'
#' This is the R binding implementation. For more information about the
#' NaviCell Web Service and a tutorial on how to use it, see
#' https://navicell.curie.fr/pages/nav_web_service.html and
#' https://github.com/eb00/RNaviCell.
#'
#' @import RCurl
#' @import RJSONIO
#' @importFrom methods new
#' @export NaviCell
#' @examples \dontrun{
#' ### Opens a communication with web service, build does not finish if example is tested
#' file<-system.file("extdata", "script.R", package = "RNaviCell")
#' source("file")
#' }
NaviCell <- setRefClass(
# class name
"NaviCell",
# Define the fields
fields = list(
proxy_url = "character",
map_url = "character",
msg_id = "numeric",
session_id = "character",
hugo_list = "vector",
packsize = "numeric"
),
# Set default values
methods = list(
initialize = function(...) {
proxy_url <<- "https://navicell.curie.fr/cgi-bin/nv_proxy.php"
map_url <<- "https://navicell.curie.fr/navicell/maps/cellcycle/master/index.php"
msg_id <<- 1000
session_id <<- ""
packsize <<- 500000
}
)
)
#------------------------------------------------------------------------------
#
# Session and utility functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
incMessageId = function(...) {
"Increase message ID counter."
msg_id <<- msg_id + 1
}
)
NaviCell$methods(
generateSessionId = function(...) {
"Generate a session ID."
.self$incMessageId()
response = postForm(.self$proxy_url, style = 'POST', id = "1", perform = "genid", msg_id = .self$msg_id, mode = "session", .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
if (response != "") {
response <- .self$formatResponse(response)
.self$session_id <- response
}
}
)
NaviCell$methods(
serverIsReady = function(...) {
"Test if NaviCell server is ready (internal utility)."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_is_ready')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style='POST', id = .self$session_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
return(fromJSON(response)$data)
}
)
NaviCell$methods(
waitForReady = function(...) {
"Wait until NaviCell server is ready (internal utility)."
for (i in 1:50) {
if (.self$serverIsReady() == TRUE) {
break
}
else {
message("wait for NaviCell server to be ready..")
Sys.sleep(1)
}
}
}
)
NaviCell$methods(
isImported = function(...) {
"Test if data table is imported (internal utility)."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_is_imported')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style='POST', id = .self$session_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
return(fromJSON(response)$data)
}
)
NaviCell$methods(
waitForImported = function(...) {
"Wait until data is imported (internal utility)."
for (i in 1:50) {
if (.self$isImported() == TRUE) {
message("data imported.")
break
}
else {
message("waiting for data to be imported...")
Sys.sleep(0.5)
}
}
}
)
NaviCell$methods(
launchBrowser = function(...) {
"Launch client browser and points to the default NaviCell map."
.self$incMessageId()
if (.self$session_id == "") {
.self$generateSessionId()
}
url <- paste(.self$map_url, '?id=', .self$session_id, sep = '')
browseURL(url)
.self$waitForReady()
}
)
NaviCell$methods(
listSessions = function(...) {
"List all NaviCell server sessions."
response <- postForm(.self$proxy_url, style='POST', id="1", perform="list", msg_id = .self$msg_id, mode="session", .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
message(response)
}
)
NaviCell$methods(
attachSession = function(session_id) {
"Attach a NaviCell server session ID."
if (.self$session_id != "") {
warning("Session id already set.")
return()
}
.self$incMessageId()
# check session id on NaviCell server
response <- postForm(.self$proxy_url, style='POST', id = session_id, msg_id = .self$msg_id, mode = 'session', perform = 'check', .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
if (response == "ok") {
.self$session_id <- session_id
}
else {
warning("Wrong session id.")
}
}
)
NaviCell$methods(
attachLastSession = function(...) {
"Attach NaviCell handle to the last existing NaviCell Web Service session."
response <- postForm(.self$proxy_url, style='POST', id = '1', msg_id = .self$msg_id, mode = 'session', perform = 'get', which = '@@', .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
message(response)
.self$attachSession(response)
}
)
NaviCell$methods(
formatResponse = function(response) {
"Format response obtained from the RCurl 'postForm' command (internal utility)."
ret = ''
if (class(response) == 'raw') {
ret <- rawToChar(response)
}
else if (class(response) == "character") {
ret <- response[1]
}
return(ret)
}
)
NaviCell$methods(
makeData = function(json_string) {
"Create NaviCell server command string from a list of parameters (internal utility)."
ret <- paste("@COMMAND ", json_string, sep = "")
return(ret)
}
)
NaviCell$methods(
formatJson = function(list_param) {
"Format list of parameters to NaviCell server compatible JSON format (internal utility)."
data <- toJSON(list_param)
# remove unnecessary characters
data <- gsub("\n", '', data)
data <- gsub(" ", "", data)
return(data)
}
)
NaviCell$methods(
file2dataString = function(fileName) {
"Load the content of a text file as tab-delimited string. Convert to NaviCell compatible format."
data_string <- NULL
data_string <- paste(readLines(fileName, warn=F),collapse='\n')
if (!is.null(data_string)) {
if (substr(data_string, nchar(data_string), nchar(data_string)) != "\n") {
data_string <- paste(data_string, '\n', sep="")
}
data_string <- paste("@DATA\n", data_string, sep="")
}
return(data_string)
}
)
#------------------------------------------------------------------------------
#
# Navigation and Zooming functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
setZoom = function(zoom_level) {
"Set a given zoom level on associated NaviCell map in browser. zoom_level = integer value."
.self$incMessageId()
list_param <- list(module='', args = array(zoom_level), msg_id = .self$msg_id, action = 'nv_set_zoom')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style='POST', id = .self$session_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
setMapCenter = function(location) {
"Set the relative position of the map center. location = 'MAP_CENTER' or 'MAP_EAST' or 'MAP_SOUTH' or MAP_NORTH' or 'MAP_SOUTH_WEST' or 'MAP_SOUTH_EAST' or 'MAP_NORTH_EAST'."
.self$incMessageId()
list_param <- list(module='', args = array(location), msg_id = .self$msg_id, action = 'nv_set_center')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
setMapCenterAbsolute = function(pos_x, pos_y) {
"Set the absolute position of the map center. x = x coordinate (integer), y = y coordinate (integer)."
.self$incMessageId()
list_param <- list(module='', args = list('ABSOLUTE', pos_x, pos_y), msg_id = .self$msg_id, action = 'nv_set_center')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
moveMapCenter = function(x, y) {
"Move the map center (relative). x = x coordinate (integer), y = y coordinate (integer)."
.self$incMessageId()
list_param <- list(module='', args = list('RELATIVE', x, y), msg_id = .self$msg_id, action = 'nv_set_center')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
#------------------------------------------------------------------------------
#
# Entity selection functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
selectEntity = function(entity) {
"Select an entity on the map. entity = entity's name (string)"
.self$incMessageId()
list_param <- list(module='', args = array(entity), msg_id = .self$msg_id, action = 'nv_find_entities')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
findEntities = function(entity, bubble) {
"Find one or more entities on the map. entity = entity's name pattern (string), bubble = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c(entity, bubble)), msg_id = .self$msg_id, action = 'nv_find_entities')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
uncheckAllEntities = function(...) {
"Uncheck all entities on the map."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_uncheck_all_entities')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
unhighlightAllEntities = function(...) {
"Uncheck all entities on the map."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_unhighlight_all_entities')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
#------------------------------------------------------------------------------
#
# Get info from NaviCell server functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
getHugoList = function(...) {
"Get the list of the HUGO gene symbols for the current map (the list is stored in the object field hugo_list."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_hugo_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#message(response)
response <- fromJSON(response)
.self$hugo_list <- response$data
return(response$data)
}
)
NaviCell$methods(
getBiotypeList = function(...) {
"Return the list of biotypes understood by NaviCell Web Service."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_biotype_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
response <- fromJSON(response)
return(response$data)
}
)
NaviCell$methods(
getModuleList = function(...) {
"Return the module list of the current NaviCell map."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_module_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
response <- fromJSON(response)
return(response$data)
}
)
NaviCell$methods(
getImportedDatatables = function(...) {
"Return the list of datatables imported in the current NaviCell session."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_datatable_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
response <- fromJSON(response)
return(response$data)
}
)
NaviCell$methods(
getImportedSamples = function(...) {
"Return the list of samples from all the datatables imported in the current NaviCell session."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_datatable_sample_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
response <- fromJSON(response)
return(response$data)
}
)
NaviCell$methods(
getImportedGenes = function(...) {
"Return the list of genes from all the datatables imported in the current NaviCell session."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_datatable_gene_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
response <- fromJSON(response)
return(response$data)
}
)
#------------------------------------------------------------------------------
#
# Datatable import functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
importDatatable = function(datatable_biotype, datatable_name, mat) {
"Import a datatable (matrix) in the current map session."
# check if the field hugo_list is set
if (length(.self$hugo_list) == 0) {
hl <- .self$getHugoList()
}
# filter matrix on hugo_list
# abort if there is no overlap
rownames(mat) %in% .self$hugo_list -> idx
if (sum(idx) < 1) {
warning("Error: no overlap between map and matrix HUGO gene symbols.")
return()
}
data_string <- NULL
# case 1: simple gene list
if (dim(mat)[2] == 0) {
# convert to list
gene_list <- rownames(mat)
sel <- gene_list[idx]
data_string <- .self$geneList2string(sel)
}
# case 2: one or more columns in the matrix
if (dim(mat)[2] > 0) {
# select rows on hugo_list
# watch out: if matrix has 1 col, return type is vector, not matrix, so cast the return to matrix.
# watch out: when matrix as only one col. colname is lost with subselect, so set it back
mat_select <- as.matrix(mat[idx,])
if (ncol(mat) == 1) {
colnames(mat_select) <- colnames(mat)
}
data_string <- .self$matrix2string(mat_select)
}
if (!is.null(data_string)) {
if (nchar(data_string) < .self$packsize) {
#print(data_string)
.self$incMessageId()
list_param <- list(module='', args = list(datatable_biotype, datatable_name, "", data_string, emptyNamedList), msg_id = .self$msg_id, action = 'nv_import_datatables')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
.self$waitForImported()
#print(.self$formatResponse(response))
}
else {
#print("size > packsize")
list_param <- list(module='', args = list(datatable_biotype, datatable_name, "", data_string, emptyNamedList), action = 'nv_import_datatables')
fill_cmd <- .self$makeData(.self$formatJson(list_param))
.self$sendBigData(fill_cmd)
.self$waitForImported()
}
}
}
)
NaviCell$methods(
sendBigData = function(fill_cmd) {
"slice data in packets big data string and send it to server (internal utility)"
cmd_len <- nchar(fill_cmd)
cmd_packcount <- as.integer(cmd_len / .self$packsize) + 1
# slice data in packets and send them to server
for (i in 0:(cmd_packcount-1)) {
cmd_packnum <- i+1
stop <- (i+1) * .self$packsize
start <- 0
if (i > 0) {
start <- (i * packsize) + 1
}
if (stop > cmd_len) {
stop <- cmd_len - 1
}
start <- start + 1
stop <- stop + 1
response <- postForm(.self$proxy_url, style = 'POST', perform = "filling", data = substr(fill_cmd, start, stop), id = .self$session_id, packcount = cmd_packcount, packnum = cmd_packnum, mode='cli2srv', .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
# end message to trigger data re-composition on server side
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', data="@@", id = .self$session_id, perform = "send_and_rcv", packcount = cmd_packcount, msg_id = .self$msg_id, mode='cli2srv', .opts=curlOptions(ssl.verifypeer=F))
}
)
NaviCell$methods(
readDatatable = function(fileName) {
"Read a data file and create an R matrix. Returns a matrix object."
mat <- as.matrix(read.table(fileName, header=T, row.names=1))
return(mat)
}
)
NaviCell$methods(
matrix2string = function(mat) {
"Convert an R matrix object to a formatted string (internal utility)."
header = ""
if (nrow(mat) == 1) {
header <- paste(colnames(mat), sep="")
}
else {
header <- paste(colnames(mat), collapse='\t', sep="")
}
string <- paste('@DATA\ngenes\t', header, sep="")
string <- paste(string, '\n', sep="")
nb_row = nrow(mat)
for (row in 1:nb_row) {
gene_name <- paste(rownames(mat)[row], '\t', sep="")
row_string = ""
if (nb_row == 1) {
row_string <- paste(mat[row], sep="")
}
else {
row_string <- paste(mat[row,], collapse='\t', sep="")
}
row_string <- paste(row_string, '\n', sep="")
string <- paste(string, gene_name, row_string, sep="")
}
return(string)
}
)
NaviCell$methods(
geneList2string = function(gene_list) {
"Convert a gene list R object to a formatted string (internal utility)."
string <- paste('@DATA\ngenes\n')
gene_string <- paste(gene_list, sep="", collapse="\n")
string <- paste(string, gene_string, sep="")
string <- paste(string, "\n", sep="")
return(string)
}
)
#------------------------------------------------------------------------------
#
# Drawing Configuration Dialog functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
drawingConfigOpen = function(...) {
"Open drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('open'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigClose = function(...) {
"Close drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('close'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigApply = function(...) {
"Apply changes to drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('apply'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigApplyAndClose = function(...) {
"Apply changes to drawing configuration and close dialog."
.self$incMessageId()
list_param <- list(module='', args = array('apply_and_close'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigCancel = function(...) {
"Cancel changes to drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('cancel'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectHeatmap = function(checked) {
"Select heatmap display in drawing configuration dialog. checked = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_heatmap', checked)), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectBarplot = function(checked) {
"Select barplot display in drawing configuration dialog. checked = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_barplot', checked)), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectGlyph = function(glyph_num, checked) {
"Select glyph display in drawing configuration dialog. glyph_num = glyph number, checked = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_glyph', glyph_num, checked)), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectMapStaining = function(checked) {
"Select map staining display in drawing configuration dialog. checked = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_map_staining', checked)), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectDisplayAllGenes= function(...) {
"Select 'Display all genes' option in drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('display_all_genes'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectDisplaySelectedGenes= function(...) {
"Select 'Display selected genes' option in drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('display_selected_genes'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# MyData Dialog functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
mydataDialogOpen = function(...) {
"Open MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('open'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogClose = function(...) {
"Close MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('close'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogSetDatatables = function(...) {
"Set Datatables tab active for MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('select_datatables'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogSetSamples = function(...) {
"Set Samples tab active for MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('select_samples'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogSetGenes = function(...) {
"Set Genes tab active for MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('select_genes'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogSetGroups = function(...) {
"Set Groups tab active for MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('select_groups'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogSetModules = function(...) {
"Set Modules tab active for MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('select_modules'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Glyph Editor functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
glyphEditorOpen = function(glyph_num) {
"Open the glyph editor. glyph_num = glyph number"
.self$incMessageId()
list_param <- list(module='', args = array(c('open', glyph_num)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorClose = function(glyph_num) {
"Close the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('close', glyph_num)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorApply = function(glyph_num) {
"Apply changes in the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply', glyph_num)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorApplyAndClose = function(glyph_num) {
"Apply changes and close the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply_and_close', glyph_num)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorCancel = function(glyph_num) {
"Cancel changes and close the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('cancel', glyph_num)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorSelectSample = function(glyph_num, sample_name) {
"Select sample or group in the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_sample', glyph_num, sample_name)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorSelectShapeDatatable = function(glyph_num, datatable_name) {
"Select datatable for glyph shape in the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable_shape', glyph_num, datatable_name)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorSelectColorDatatable = function(glyph_num, datatable_name) {
"Select datatable for glyph color in the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable_color', glyph_num, datatable_name)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorSelectSizeDatatable = function(glyph_num, datatable_name) {
"Select datatable for glyph size in the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable_size', glyph_num, datatable_name)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorSetTransparency = function(glyph_num, value) {
"Set transparency parameter in the glyph editor. value = integer between 1 and 100."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_transparency', glyph_num, value)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Barplot Editor functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
barplotEditorOpen = function(...) {
"Open the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('open'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorClose = function(...) {
"Close the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('close'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorApply = function(...) {
"Apply changes for the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('apply'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorApplyAndClose = function(...) {
"Apply changes and close the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('apply_and_close'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorCancel = function(...) {
"Cancel changes and close the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('cancel'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorSelectSample = function(col_num, sample_name) {
"Select a sample or a group in the barplot editor. col_num = column index number, sample_name = sample or group name"
.self$incMessageId()
list_param <- list(module='', args = array(c('select_sample', col_num, sample_name)), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorSelectDatatable = function(datatable_name) {
"Select a datatable in the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable', datatable_name)), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorClearSamples = function(...) {
"Clear all samples in the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('clear_samples'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorSelectAllSamples = function(...) {
"Select all samples in the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('all_samples'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorSelectAllGroups = function(...) {
"Select all groups in the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('all_groups'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorSetTransparency = function(value) {
"Select transparency parameter in the barplot editor. value = integer between 1 and 100"
.self$incMessageId()
list_param <- list(module='', args = array(c('set_transparency', value)), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Heatmap Editor functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
heatmapEditorOpen = function(...) {
"Open the heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('open'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorClose = function(...) {
"Close the heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('close'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorCancel = function(...) {
"Cancel changes and close the heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('cancel'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorApply = function(...) {
"Apply changes for the heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('apply'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorApplyAndClose = function(...) {
"Apply changes and close the heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('apply_and_close'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorSelectSample = function(col_num, sample_name) {
"Select sample or group in heatmap editor. col_num = editor column number, sample_name = sample or group name."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_sample', col_num, sample_name)), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorSelectDatatable = function(row_num, datatable_name) {
"Select datatable in heatmap editor. row_num = editor row number."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable', row_num, datatable_name)), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorClearSamples = function(...) {
"Clear all samples in heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('clear_samples'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorSelectAllSamples = function(...) {
"Select all samples in heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('all_samples'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorSelectAllGroups = function(...) {
"Select all groups in heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('all_groups'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorSetTransparency = function(value) {
"Set transparency parameter in heatmap editor. value = integer between 1 and 100."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_transparency', value)), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Unordered Discrete Configuration Editor functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
unorderedConfigOpen = function(datatable_name, datatable_parameter) {
"Open unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('open', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigClose = function(datatable_name, datatable_parameter) {
"Open unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('close', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigCancel= function(datatable_name, datatable_parameter) {
"Cancel changes for unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('cancel', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigApply = function(datatable_name, datatable_parameter) {
"Apply changes to unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigApplyAndClose = function(datatable_name, datatable_parameter) {
"Apply changes to unordered discrete configuration editor for a given type of parameter, and close the window. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply_and_close', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetAdvancedConfig = function(datatable_name, datatable_parameter, checked) {
"Open/close advanced configuration for unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_advanced_configuration', datatable_name, datatable_parameter, checked)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetDiscreteValue= function(datatable_name, datatable_parameter, sample_or_group, index, value) {
"Set discrete value for unordered discrete configuration editor for a given
type of parameter. datatable_parameter = 'shape' or
'color' or 'size', sample_or_group = 'sample' or 'group', index = integer,
value = double."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_discrete_value', datatable_name, datatable_parameter, sample_or_group, index, value)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetDiscreteColor= function(datatable_name, sample_or_group, index, color) {
"Set color value for unordered discrete configuration editor. sample_or_group = 'sample' or 'group', index = integer, color = string hex code color value, e.g. 'FF0000'."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_discrete_color', datatable_name, "color", sample_or_group, index, color)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetDiscreteSize= function(datatable_name, sample_or_group, index, size) {
"Set size value for unordered discrete configuration editor. sample_or_group = 'sample' or 'group', index = integer, size = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_discrete_size', datatable_name, "size", sample_or_group, index, size)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetDiscreteShape = function(datatable_name, sample_or_group, index, shape) {
"Set shape value for unordered discrete configuration editor. sample_or_group = 'sample' or 'group', index = integer, shape = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_discrete_shape', datatable_name, "shape", sample_or_group, index, shape)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetDiscreteCondition = function(datatable_name, datatable_parameter, sample_or_group, index, condition) {
"Set condition value for unordered discrete configuration editor. datatable_parameter = 'size' or 'shape' or 'color'. sample_or_group = 'sample' or 'group', index = integer, condition = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_discrete_cond', datatable_name, datatable_parameter, sample_or_group, index, condition)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSwitchSampleTab = function(datatable_name, datatable_parameter) {
"Switch to sample tab for unordered discrete configuration editor. datatable_parameter = 'size' or 'shape' or 'color'."
.self$incMessageId()
list_param <- list(module='', args = array(c('switch_sample_tab', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSwitchGroupTab = function(datatable_name, datatable_parameter) {
"Switch to group tab for unordered discrete configuration editor. datatable_parameter = 'size' or 'shape' or 'color'."
.self$incMessageId()
list_param <- list(module='', args = array(c('switch_group_tab', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Continuous Configuration Editor functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
continuousConfigOpen = function(datatable_name, datatable_parameter) {
"Open continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('open', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigClose = function(datatable_name, datatable_parameter) {
"Close continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('close', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigApplyAndClose = function(datatable_name, datatable_parameter) {
"Apply changes and close continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply_and_close', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigCancelAndClose = function(datatable_name, datatable_parameter) {
"Cancel changes and close continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('cancel', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetAbsVal = function(datatable_parameter, datatable_name, checked) {
"Set absolute value mode for continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size', checked = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_sample_absval', datatable_parameter, datatable_name, checked)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetSampleMethod = function(datatable_parameter, datatable_name, method_index) {
"Set the method used when multiple symbols map to the same entity. datatable_parameter = 'shape' or 'color' or 'size', method_index = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_sample_method', datatable_parameter, datatable_name, method_index)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetGroupMethod = function(datatable_parameter, datatable_name, method_index) {
"Set the method used when multiple symbols map to the same entity. datatable_parameter = 'shape' or 'color' or 'size', method_index = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_group_method', datatable_parameter, datatable_name, method_index)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetSelectionSize = function(datatable_name, sample_or_group, index, size) {
"Set the size selection to a given value for the 'size' parameter. sample_or_group = 'sample' or 'group', index = integer, size = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_select_size', datatable_name, "size", sample_or_group, index, size)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetSelectionShape = function(datatable_name, sample_or_group, index, shape) {
"Set the shape selection to a given value for the 'shape' parameter. sample_or_group = 'sample' or 'group', index = integer, shape = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_select_shape', datatable_name, "shape", sample_or_group, index, shape)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSwitchSampleTab = function(datatable_name, datatable_parameter) {
"Switch continuous configuration editor window to 'sample' tab. Parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('switch_sample_tab', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSwitchGroupTab = function(datatable_name, datatable_parameter) {
"Switch continuous configuration editor window to 'group' tab. Parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('switch_group_tab', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetStepCount = function(sample_or_group, datatable_parameter, datatable_name, step_count) {
"Set continuous configuration step count parameter to a given value. sample_or_group = 'sample' or 'group'. parameter = 'shape' or 'color' or 'size' step_count = integer value."
.self$incMessageId()
list_param <- list(module='', args = array(c('step_count_change', sample_or_group, datatable_parameter, datatable_name, step_count)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetColorAt = function(datatable_name, sample_or_group, index, color_hex_value) {
"Set continuous configuration color value. sample_or_group = 'sample' or 'group'."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_input_color', datatable_name, 'color', sample_or_group, index, color_hex_value)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetValueAt = function(datatable_name, parameter_type, sample_or_group, index, continuous_value) {
"Set continuous configuration continuous value at a given index. sample_or_group = 'sample' or 'group'. parameter_type = 'size' or 'shape' or 'color'. "
.self$incMessageId()
list_param <- list(module='', args = array(c('set_input_value', datatable_name, parameter_type, sample_or_group, index, continuous_value)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigApply = function(datatable_name, parameter_type) {
"Apply changes to the continuous configuration editor. parameter_type = 'size' or 'shape' or 'color'. "
.self$incMessageId()
list_param <- list(module='', args = array(c('apply', datatable_name, parameter_type)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Map Staining functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
mapStainingEditorSelectDatatable = function(datatable_name) {
"Select a datatable for the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable', datatable_name)), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorSelectSample = function(sample_name) {
"Select a sample for the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_sample', sample_name)), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorApply = function(...) {
"Apply modifications for the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply')), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorCancel = function(...) {
"Cancel modifications and close the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('cancel')), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorOpen = function(...) {
"Open the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array('open'), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorClose = function(...) {
"Close the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('close')), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorApplyAndClose = function(...) {
"Apply changes and close the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply_and_close')), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorSetTransparency = function(transparency_value) {
"Set the transparency value parameter for the map staining editor (integer value between 1 and 100)."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_transparency'), transparency_value), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Sample Annotation functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
importSampleAnnotationFromFile = function(fileName) {
data_string <- .self$file2dataString(fileName)
if (!is.null(data_string)) {
if (nchar(data_string) < .self$packsize) {
.self$incMessageId()
list_param <- list(module='', args = list("import", data_string), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
else {
list_param <- list(module='', args = list("import", data_string), action = 'nv_sample_annotation_perform')
fill_cmd <- .self$makeData(.self$formatJson(list_param))
.self$sendBigData(fill_cmd)
.self$waitForImported()
}
}
}
)
NaviCell$methods(
sampleAnnotationSelectAnnotation = function(annotation_name, true_or_false) {
"Select or un-select an annotation for creating groups from a sample annotation table. true_or_false = TRUE, select, true_or_false = FALSE, un-select."
.self$incMessageId()
list_param <- list(module='', args = list("select_annotation", annotation_name, true_or_false), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
sampleAnnotationApply = function(...) {
"Apply the modifications done on a sample annotation table."
.self$incMessageId()
list_param <- list(module='', args = list("apply"), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
sampleAnnotationOpen = function(...) {
"Open sample annotation dialog."
.self$incMessageId()
list_param <- list(module='', args = list("open"), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
sampleAnnotationClose = function(...) {
"Close sample annotation dialog."
.self$incMessageId()
list_param <- list(module='', args = list("close"), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
sampleAnnotationCancel = function(...) {
"Cancel changes and close sample annotation dialog."
.self$incMessageId()
list_param <- list(module='', args = list("cancel"), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
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# RNaviCell package
#
# Copyright (C) {2015} {Institut Curie, 26 rue d'Ulm, 75005 Paris}
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library 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
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301
# USA
#' NaviCell reference class
#'
#' NaviCell (https://navicell.curie.fr) is a web-based environment for
#' browsing, commenting and analyzing very large biological molecular networks
#' using Google Maps and for visualizing 'omics' data on top of the network
#' maps.
#'
#' NaviCell can also act as a server allowing to be remotely controlled through
#' a REST API. A python and a R language bindings have been developped on top
#' of the REST API to hide technical details and to provide users and
#' programmers a friendly interface. A Java binding has been initiated.
#'
#' This is the R binding implementation. For more information about the
#' NaviCell Web Service and a tutorial on how to use it, see
#' https://navicell.curie.fr/pages/nav_web_service.html and
#' https://github.com/eb00/RNaviCell.
#'
#' @import RCurl
#' @import RJSONIO
#' @importFrom methods new
#' @export NaviCell
#' @examples \dontrun{
#' ### Opens a communication with web service, build does not finish if example is tested
#' file<-system.file("extdata", "script.R", package = "RNaviCell")
#' source("file")
#' }
NaviCell <- setRefClass(
# class name
"NaviCell",
# Define the fields
fields = list(
proxy_url = "character",
map_url = "character",
msg_id = "numeric",
session_id = "character",
hugo_list = "vector",
packsize = "numeric"
),
# Set default values
methods = list(
initialize = function(...) {
proxy_url <<- "https://navicell.curie.fr/cgi-bin/nv_proxy.php"
map_url <<- "https://navicell.curie.fr/navicell/maps/cellcycle/master/index.php"
msg_id <<- 1000
session_id <<- ""
packsize <<- 500000
}
)
)
#------------------------------------------------------------------------------
#
# Session and utility functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
incMessageId = function(...) {
"Increase message ID counter."
msg_id <<- msg_id + 1
}
)
NaviCell$methods(
generateSessionId = function(...) {
"Generate a session ID."
.self$incMessageId()
response = postForm(.self$proxy_url, style = 'POST', id = "1", perform = "genid", msg_id = .self$msg_id, mode = "session", .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
if (response != "") {
response <- .self$formatResponse(response)
.self$session_id <- response
}
}
)
NaviCell$methods(
serverIsReady = function(...) {
"Test if NaviCell server is ready (internal utility)."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_is_ready')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style='POST', id = .self$session_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
return(fromJSON(response)$data)
}
)
NaviCell$methods(
waitForReady = function(...) {
"Wait until NaviCell server is ready (internal utility)."
for (i in 1:50) {
if (.self$serverIsReady() == TRUE) {
break
}
else {
message("wait for NaviCell server to be ready..")
Sys.sleep(1)
}
}
}
)
NaviCell$methods(
isImported = function(...) {
"Test if data table is imported (internal utility)."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_is_imported')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style='POST', id = .self$session_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
return(fromJSON(response)$data)
}
)
NaviCell$methods(
waitForImported = function(...) {
"Wait until data is imported (internal utility)."
for (i in 1:50) {
if (.self$isImported() == TRUE) {
message("data imported.")
break
}
else {
message("waiting for data to be imported...")
Sys.sleep(0.5)
}
}
}
)
NaviCell$methods(
launchBrowser = function(...) {
"Launch client browser and points to the default NaviCell map."
.self$incMessageId()
if (.self$session_id == "") {
.self$generateSessionId()
}
url <- paste(.self$map_url, '?id=', .self$session_id, sep = '')
browseURL(url)
.self$waitForReady()
}
)
NaviCell$methods(
listSessions = function(...) {
"List all NaviCell server sessions."
response <- postForm(.self$proxy_url, style='POST', id="1", perform="list", msg_id = .self$msg_id, mode="session", .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
message(response)
}
)
NaviCell$methods(
attachSession = function(session_id) {
"Attach a NaviCell server session ID."
if (.self$session_id != "") {
warning("Session id already set.")
return()
}
.self$incMessageId()
# check session id on NaviCell server
response <- postForm(.self$proxy_url, style='POST', id = session_id, msg_id = .self$msg_id, mode = 'session', perform = 'check', .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
if (response == "ok") {
.self$session_id <- session_id
}
else {
warning("Wrong session id.")
}
}
)
NaviCell$methods(
attachLastSession = function(...) {
"Attach NaviCell handle to the last existing NaviCell Web Service session."
response <- postForm(.self$proxy_url, style='POST', id = '1', msg_id = .self$msg_id, mode = 'session', perform = 'get', which = '@@', .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
message(response)
.self$attachSession(response)
}
)
NaviCell$methods(
formatResponse = function(response) {
"Format response obtained from the RCurl 'postForm' command (internal utility)."
ret = ''
if (class(response) == 'raw') {
ret <- rawToChar(response)
}
else if (class(response) == "character") {
ret <- response[1]
}
return(ret)
}
)
NaviCell$methods(
makeData = function(json_string) {
"Create NaviCell server command string from a list of parameters (internal utility)."
ret <- paste("@COMMAND ", json_string, sep = "")
return(ret)
}
)
NaviCell$methods(
formatJson = function(list_param) {
"Format list of parameters to NaviCell server compatible JSON format (internal utility)."
data <- toJSON(list_param)
# remove unnecessary characters
data <- gsub("\n", '', data)
data <- gsub(" ", "", data)
return(data)
}
)
NaviCell$methods(
file2dataString = function(fileName) {
"Load the content of a text file as tab-delimited string. Convert to NaviCell compatible format."
data_string <- NULL
data_string <- paste(readLines(fileName, warn=F),collapse='\n')
if (!is.null(data_string)) {
if (substr(data_string, nchar(data_string), nchar(data_string)) != "\n") {
data_string <- paste(data_string, '\n', sep="")
}
data_string <- paste("@DATA\n", data_string, sep="")
}
return(data_string)
}
)
#------------------------------------------------------------------------------
#
# Navigation and Zooming functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
setZoom = function(zoom_level) {
"Set a given zoom level on associated NaviCell map in browser. zoom_level = integer value."
.self$incMessageId()
list_param <- list(module='', args = array(zoom_level), msg_id = .self$msg_id, action = 'nv_set_zoom')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style='POST', id = .self$session_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
setMapCenter = function(location) {
"Set the relative position of the map center. location = 'MAP_CENTER' or 'MAP_EAST' or 'MAP_SOUTH' or MAP_NORTH' or 'MAP_SOUTH_WEST' or 'MAP_SOUTH_EAST' or 'MAP_NORTH_EAST'."
.self$incMessageId()
list_param <- list(module='', args = array(location), msg_id = .self$msg_id, action = 'nv_set_center')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
setMapCenterAbsolute = function(pos_x, pos_y) {
"Set the absolute position of the map center. x = x coordinate (integer), y = y coordinate (integer)."
.self$incMessageId()
list_param <- list(module='', args = list('ABSOLUTE', pos_x, pos_y), msg_id = .self$msg_id, action = 'nv_set_center')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
moveMapCenter = function(x, y) {
"Move the map center (relative). x = x coordinate (integer), y = y coordinate (integer)."
.self$incMessageId()
list_param <- list(module='', args = list('RELATIVE', x, y), msg_id = .self$msg_id, action = 'nv_set_center')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
#------------------------------------------------------------------------------
#
# Entity selection functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
selectEntity = function(entity) {
"Select an entity on the map. entity = entity's name (string)"
.self$incMessageId()
list_param <- list(module='', args = array(entity), msg_id = .self$msg_id, action = 'nv_find_entities')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
findEntities = function(entity, bubble) {
"Find one or more entities on the map. entity = entity's name pattern (string), bubble = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c(entity, bubble)), msg_id = .self$msg_id, action = 'nv_find_entities')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
uncheckAllEntities = function(...) {
"Uncheck all entities on the map."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_uncheck_all_entities')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
NaviCell$methods(
unhighlightAllEntities = function(...) {
"Uncheck all entities on the map."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_unhighlight_all_entities')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#print(response)
}
)
#------------------------------------------------------------------------------
#
# Get info from NaviCell server functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
getHugoList = function(...) {
"Get the list of the HUGO gene symbols for the current map (the list is stored in the object field hugo_list."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_hugo_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
#message(response)
response <- fromJSON(response)
.self$hugo_list <- response$data
return(response$data)
}
)
NaviCell$methods(
getBiotypeList = function(...) {
"Return the list of biotypes understood by NaviCell Web Service."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_biotype_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
response <- fromJSON(response)
return(response$data)
}
)
NaviCell$methods(
getModuleList = function(...) {
"Return the module list of the current NaviCell map."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_module_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
response <- fromJSON(response)
return(response$data)
}
)
NaviCell$methods(
getImportedDatatables = function(...) {
"Return the list of datatables imported in the current NaviCell session."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_datatable_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
response <- fromJSON(response)
return(response$data)
}
)
NaviCell$methods(
getImportedSamples = function(...) {
"Return the list of samples from all the datatables imported in the current NaviCell session."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_datatable_sample_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
response <- fromJSON(response)
return(response$data)
}
)
NaviCell$methods(
getImportedGenes = function(...) {
"Return the list of genes from all the datatables imported in the current NaviCell session."
.self$incMessageId()
list_param <- list(module='', args = array(), msg_id = .self$msg_id, action = 'nv_get_datatable_gene_list')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
response <- .self$formatResponse(response)
response <- fromJSON(response)
return(response$data)
}
)
#------------------------------------------------------------------------------
#
# Datatable import functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
importDatatable = function(datatable_biotype, datatable_name, mat) {
"Import a datatable (matrix) in the current map session."
# check if the field hugo_list is set
if (length(.self$hugo_list) == 0) {
hl <- .self$getHugoList()
}
# filter matrix on hugo_list
# abort if there is no overlap
rownames(mat) %in% .self$hugo_list -> idx
if (sum(idx) < 1) {
warning("Error: no overlap between map and matrix HUGO gene symbols.")
return()
}
data_string <- NULL
# case 1: simple gene list
if (dim(mat)[2] == 0) {
# convert to list
gene_list <- rownames(mat)
sel <- gene_list[idx]
data_string <- .self$geneList2string(sel)
}
# case 2: one or more columns in the matrix
if (dim(mat)[2] > 0) {
# select rows on hugo_list
# watch out: if matrix has 1 col, return type is vector, not matrix, so cast the return to matrix.
# watch out: when matrix as only one col. colname is lost with subselect, so set it back
mat_select <- as.matrix(mat[idx,])
if (ncol(mat) == 1) {
colnames(mat_select) <- colnames(mat)
}
data_string <- .self$matrix2string(mat_select)
}
if (!is.null(data_string)) {
if (nchar(data_string) < .self$packsize) {
#print(data_string)
.self$incMessageId()
list_param <- list(module='', args = list(datatable_biotype, datatable_name, "", data_string, emptyNamedList), msg_id = .self$msg_id, action = 'nv_import_datatables')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
.self$waitForImported()
#print(.self$formatResponse(response))
}
else {
#print("size > packsize")
list_param <- list(module='', args = list(datatable_biotype, datatable_name, "", data_string, emptyNamedList), action = 'nv_import_datatables')
fill_cmd <- .self$makeData(.self$formatJson(list_param))
.self$sendBigData(fill_cmd)
.self$waitForImported()
}
}
}
)
NaviCell$methods(
sendBigData = function(fill_cmd) {
"slice data in packets big data string and send it to server (internal utility)"
cmd_len <- nchar(fill_cmd)
cmd_packcount <- as.integer(cmd_len / .self$packsize) + 1
# slice data in packets and send them to server
for (i in 0:(cmd_packcount-1)) {
cmd_packnum <- i+1
stop <- (i+1) * .self$packsize
start <- 0
if (i > 0) {
start <- (i * packsize) + 1
}
if (stop > cmd_len) {
stop <- cmd_len - 1
}
start <- start + 1
stop <- stop + 1
response <- postForm(.self$proxy_url, style = 'POST', perform = "filling", data = substr(fill_cmd, start, stop), id = .self$session_id, packcount = cmd_packcount, packnum = cmd_packnum, mode='cli2srv', .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
# end message to trigger data re-composition on server side
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', data="@@", id = .self$session_id, perform = "send_and_rcv", packcount = cmd_packcount, msg_id = .self$msg_id, mode='cli2srv', .opts=curlOptions(ssl.verifypeer=F))
}
)
NaviCell$methods(
readDatatable = function(fileName) {
"Read a data file and create an R matrix. Returns a matrix object."
mat <- as.matrix(read.table(fileName, header=T, row.names=1))
return(mat)
}
)
NaviCell$methods(
matrix2string = function(mat) {
"Convert an R matrix object to a formatted string (internal utility)."
header = ""
if (nrow(mat) == 1) {
header <- paste(colnames(mat), sep="")
}
else {
header <- paste(colnames(mat), collapse='\t', sep="")
}
string <- paste('@DATA\ngenes\t', header, sep="")
string <- paste(string, '\n', sep="")
nb_row = nrow(mat)
for (row in 1:nb_row) {
gene_name <- paste(rownames(mat)[row], '\t', sep="")
row_string = ""
if (nb_row == 1) {
row_string <- paste(mat[row], sep="")
}
else {
row_string <- paste(mat[row,], collapse='\t', sep="")
}
row_string <- paste(row_string, '\n', sep="")
string <- paste(string, gene_name, row_string, sep="")
}
return(string)
}
)
NaviCell$methods(
geneList2string = function(gene_list) {
"Convert a gene list R object to a formatted string (internal utility)."
string <- paste('@DATA\ngenes\n')
gene_string <- paste(gene_list, sep="", collapse="\n")
string <- paste(string, gene_string, sep="")
string <- paste(string, "\n", sep="")
return(string)
}
)
#------------------------------------------------------------------------------
#
# Drawing Configuration Dialog functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
drawingConfigOpen = function(...) {
"Open drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('open'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigClose = function(...) {
"Close drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('close'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigApply = function(...) {
"Apply changes to drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('apply'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigApplyAndClose = function(...) {
"Apply changes to drawing configuration and close dialog."
.self$incMessageId()
list_param <- list(module='', args = array('apply_and_close'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigCancel = function(...) {
"Cancel changes to drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('cancel'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectHeatmap = function(checked) {
"Select heatmap display in drawing configuration dialog. checked = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_heatmap', checked)), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectBarplot = function(checked) {
"Select barplot display in drawing configuration dialog. checked = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_barplot', checked)), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectGlyph = function(glyph_num, checked) {
"Select glyph display in drawing configuration dialog. glyph_num = glyph number, checked = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_glyph', glyph_num, checked)), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectMapStaining = function(checked) {
"Select map staining display in drawing configuration dialog. checked = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_map_staining', checked)), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectDisplayAllGenes= function(...) {
"Select 'Display all genes' option in drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('display_all_genes'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
drawingConfigSelectDisplaySelectedGenes= function(...) {
"Select 'Display selected genes' option in drawing configuration dialog."
.self$incMessageId()
list_param <- list(module='', args = array('display_selected_genes'), msg_id = .self$msg_id, action = 'nv_drawing_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# MyData Dialog functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
mydataDialogOpen = function(...) {
"Open MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('open'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogClose = function(...) {
"Close MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('close'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogSetDatatables = function(...) {
"Set Datatables tab active for MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('select_datatables'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogSetSamples = function(...) {
"Set Samples tab active for MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('select_samples'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogSetGenes = function(...) {
"Set Genes tab active for MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('select_genes'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogSetGroups = function(...) {
"Set Groups tab active for MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('select_groups'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mydataDialogSetModules = function(...) {
"Set Modules tab active for MyData Dialog."
.self$incMessageId()
list_param <- list(module='', args = array('select_modules'), msg_id = .self$msg_id, action = 'nv_mydata_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Glyph Editor functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
glyphEditorOpen = function(glyph_num) {
"Open the glyph editor. glyph_num = glyph number"
.self$incMessageId()
list_param <- list(module='', args = array(c('open', glyph_num)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorClose = function(glyph_num) {
"Close the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('close', glyph_num)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorApply = function(glyph_num) {
"Apply changes in the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply', glyph_num)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorApplyAndClose = function(glyph_num) {
"Apply changes and close the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply_and_close', glyph_num)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorCancel = function(glyph_num) {
"Cancel changes and close the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('cancel', glyph_num)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorSelectSample = function(glyph_num, sample_name) {
"Select sample or group in the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_sample', glyph_num, sample_name)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorSelectShapeDatatable = function(glyph_num, datatable_name) {
"Select datatable for glyph shape in the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable_shape', glyph_num, datatable_name)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorSelectColorDatatable = function(glyph_num, datatable_name) {
"Select datatable for glyph color in the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable_color', glyph_num, datatable_name)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorSelectSizeDatatable = function(glyph_num, datatable_name) {
"Select datatable for glyph size in the glyph editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable_size', glyph_num, datatable_name)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
glyphEditorSetTransparency = function(glyph_num, value) {
"Set transparency parameter in the glyph editor. value = integer between 1 and 100."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_transparency', glyph_num, value)), msg_id = .self$msg_id, action = 'nv_glyph_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Barplot Editor functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
barplotEditorOpen = function(...) {
"Open the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('open'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorClose = function(...) {
"Close the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('close'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorApply = function(...) {
"Apply changes for the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('apply'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorApplyAndClose = function(...) {
"Apply changes and close the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('apply_and_close'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorCancel = function(...) {
"Cancel changes and close the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('cancel'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorSelectSample = function(col_num, sample_name) {
"Select a sample or a group in the barplot editor. col_num = column index number, sample_name = sample or group name"
.self$incMessageId()
list_param <- list(module='', args = array(c('select_sample', col_num, sample_name)), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorSelectDatatable = function(datatable_name) {
"Select a datatable in the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable', datatable_name)), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorClearSamples = function(...) {
"Clear all samples in the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('clear_samples'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorSelectAllSamples = function(...) {
"Select all samples in the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('all_samples'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorSelectAllGroups = function(...) {
"Select all groups in the barplot editor."
.self$incMessageId()
list_param <- list(module='', args = array('all_groups'), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
barplotEditorSetTransparency = function(value) {
"Select transparency parameter in the barplot editor. value = integer between 1 and 100"
.self$incMessageId()
list_param <- list(module='', args = array(c('set_transparency', value)), msg_id = .self$msg_id, action = 'nv_barplot_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Heatmap Editor functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
heatmapEditorOpen = function(...) {
"Open the heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('open'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorClose = function(...) {
"Close the heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('close'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorCancel = function(...) {
"Cancel changes and close the heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('cancel'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorApply = function(...) {
"Apply changes for the heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('apply'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorApplyAndClose = function(...) {
"Apply changes and close the heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('apply_and_close'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorSelectSample = function(col_num, sample_name) {
"Select sample or group in heatmap editor. col_num = editor column number, sample_name = sample or group name."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_sample', col_num, sample_name)), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorSelectDatatable = function(row_num, datatable_name) {
"Select datatable in heatmap editor. row_num = editor row number."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable', row_num, datatable_name)), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorClearSamples = function(...) {
"Clear all samples in heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('clear_samples'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorSelectAllSamples = function(...) {
"Select all samples in heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('all_samples'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorSelectAllGroups = function(...) {
"Select all groups in heatmap editor."
.self$incMessageId()
list_param <- list(module='', args = array('all_groups'), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
heatmapEditorSetTransparency = function(value) {
"Set transparency parameter in heatmap editor. value = integer between 1 and 100."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_transparency', value)), msg_id = .self$msg_id, action = 'nv_heatmap_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Unordered Discrete Configuration Editor functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
unorderedConfigOpen = function(datatable_name, datatable_parameter) {
"Open unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('open', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigClose = function(datatable_name, datatable_parameter) {
"Open unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('close', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigCancel= function(datatable_name, datatable_parameter) {
"Cancel changes for unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('cancel', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigApply = function(datatable_name, datatable_parameter) {
"Apply changes to unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigApplyAndClose = function(datatable_name, datatable_parameter) {
"Apply changes to unordered discrete configuration editor for a given type of parameter, and close the window. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply_and_close', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetAdvancedConfig = function(datatable_name, datatable_parameter, checked) {
"Open/close advanced configuration for unordered discrete configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_advanced_configuration', datatable_name, datatable_parameter, checked)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetDiscreteValue= function(datatable_name, datatable_parameter, sample_or_group, index, value) {
"Set discrete value for unordered discrete configuration editor for a given
type of parameter. datatable_parameter = 'shape' or
'color' or 'size', sample_or_group = 'sample' or 'group', index = integer,
value = double."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_discrete_value', datatable_name, datatable_parameter, sample_or_group, index, value)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetDiscreteColor= function(datatable_name, sample_or_group, index, color) {
"Set color value for unordered discrete configuration editor. sample_or_group = 'sample' or 'group', index = integer, color = string hex code color value, e.g. 'FF0000'."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_discrete_color', datatable_name, "color", sample_or_group, index, color)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetDiscreteSize= function(datatable_name, sample_or_group, index, size) {
"Set size value for unordered discrete configuration editor. sample_or_group = 'sample' or 'group', index = integer, size = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_discrete_size', datatable_name, "size", sample_or_group, index, size)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetDiscreteShape = function(datatable_name, sample_or_group, index, shape) {
"Set shape value for unordered discrete configuration editor. sample_or_group = 'sample' or 'group', index = integer, shape = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_discrete_shape', datatable_name, "shape", sample_or_group, index, shape)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSetDiscreteCondition = function(datatable_name, datatable_parameter, sample_or_group, index, condition) {
"Set condition value for unordered discrete configuration editor. datatable_parameter = 'size' or 'shape' or 'color'. sample_or_group = 'sample' or 'group', index = integer, condition = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_discrete_cond', datatable_name, datatable_parameter, sample_or_group, index, condition)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSwitchSampleTab = function(datatable_name, datatable_parameter) {
"Switch to sample tab for unordered discrete configuration editor. datatable_parameter = 'size' or 'shape' or 'color'."
.self$incMessageId()
list_param <- list(module='', args = array(c('switch_sample_tab', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
unorderedConfigSwitchGroupTab = function(datatable_name, datatable_parameter) {
"Switch to group tab for unordered discrete configuration editor. datatable_parameter = 'size' or 'shape' or 'color'."
.self$incMessageId()
list_param <- list(module='', args = array(c('switch_group_tab', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_unordered_discrete_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Continuous Configuration Editor functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
continuousConfigOpen = function(datatable_name, datatable_parameter) {
"Open continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('open', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigClose = function(datatable_name, datatable_parameter) {
"Close continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('close', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigApplyAndClose = function(datatable_name, datatable_parameter) {
"Apply changes and close continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply_and_close', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigCancelAndClose = function(datatable_name, datatable_parameter) {
"Cancel changes and close continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('cancel', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetAbsVal = function(datatable_parameter, datatable_name, checked) {
"Set absolute value mode for continuous configuration editor for a given type of parameter. datatable_parameter = 'shape' or 'color' or 'size', checked = TRUE or FALSE."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_sample_absval', datatable_parameter, datatable_name, checked)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetSampleMethod = function(datatable_parameter, datatable_name, method_index) {
"Set the method used when multiple symbols map to the same entity. datatable_parameter = 'shape' or 'color' or 'size', method_index = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_sample_method', datatable_parameter, datatable_name, method_index)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetGroupMethod = function(datatable_parameter, datatable_name, method_index) {
"Set the method used when multiple symbols map to the same entity. datatable_parameter = 'shape' or 'color' or 'size', method_index = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_group_method', datatable_parameter, datatable_name, method_index)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetSelectionSize = function(datatable_name, sample_or_group, index, size) {
"Set the size selection to a given value for the 'size' parameter. sample_or_group = 'sample' or 'group', index = integer, size = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_select_size', datatable_name, "size", sample_or_group, index, size)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetSelectionShape = function(datatable_name, sample_or_group, index, shape) {
"Set the shape selection to a given value for the 'shape' parameter. sample_or_group = 'sample' or 'group', index = integer, shape = integer."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_select_shape', datatable_name, "shape", sample_or_group, index, shape)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSwitchSampleTab = function(datatable_name, datatable_parameter) {
"Switch continuous configuration editor window to 'sample' tab. Parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('switch_sample_tab', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSwitchGroupTab = function(datatable_name, datatable_parameter) {
"Switch continuous configuration editor window to 'group' tab. Parameter = 'shape' or 'color' or 'size'."
.self$incMessageId()
list_param <- list(module='', args = array(c('switch_group_tab', datatable_name, datatable_parameter)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetStepCount = function(sample_or_group, datatable_parameter, datatable_name, step_count) {
"Set continuous configuration step count parameter to a given value. sample_or_group = 'sample' or 'group'. parameter = 'shape' or 'color' or 'size' step_count = integer value."
.self$incMessageId()
list_param <- list(module='', args = array(c('step_count_change', sample_or_group, datatable_parameter, datatable_name, step_count)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetColorAt = function(datatable_name, sample_or_group, index, color_hex_value) {
"Set continuous configuration color value. sample_or_group = 'sample' or 'group'."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_input_color', datatable_name, 'color', sample_or_group, index, color_hex_value)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigSetValueAt = function(datatable_name, parameter_type, sample_or_group, index, continuous_value) {
"Set continuous configuration continuous value at a given index. sample_or_group = 'sample' or 'group'. parameter_type = 'size' or 'shape' or 'color'. "
.self$incMessageId()
list_param <- list(module='', args = array(c('set_input_value', datatable_name, parameter_type, sample_or_group, index, continuous_value)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
continuousConfigApply = function(datatable_name, parameter_type) {
"Apply changes to the continuous configuration editor. parameter_type = 'size' or 'shape' or 'color'. "
.self$incMessageId()
list_param <- list(module='', args = array(c('apply', datatable_name, parameter_type)), msg_id = .self$msg_id, action = 'nv_display_continuous_config_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Map Staining functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
mapStainingEditorSelectDatatable = function(datatable_name) {
"Select a datatable for the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_datatable', datatable_name)), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorSelectSample = function(sample_name) {
"Select a sample for the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('select_sample', sample_name)), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorApply = function(...) {
"Apply modifications for the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply')), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorCancel = function(...) {
"Cancel modifications and close the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('cancel')), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorOpen = function(...) {
"Open the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array('open'), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorClose = function(...) {
"Close the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('close')), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorApplyAndClose = function(...) {
"Apply changes and close the map staining editor."
.self$incMessageId()
list_param <- list(module='', args = array(c('apply_and_close')), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
mapStainingEditorSetTransparency = function(transparency_value) {
"Set the transparency value parameter for the map staining editor (integer value between 1 and 100)."
.self$incMessageId()
list_param <- list(module='', args = array(c('set_transparency'), transparency_value), msg_id = .self$msg_id, action = 'nv_map_staining_editor_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
#------------------------------------------------------------------------------
#
# Sample Annotation functions
#
#------------------------------------------------------------------------------
NaviCell$methods(
importSampleAnnotationFromFile = function(fileName) {
data_string <- .self$file2dataString(fileName)
if (!is.null(data_string)) {
if (nchar(data_string) < .self$packsize) {
.self$incMessageId()
list_param <- list(module='', args = list("import", data_string), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
else {
list_param <- list(module='', args = list("import", data_string), action = 'nv_sample_annotation_perform')
fill_cmd <- .self$makeData(.self$formatJson(list_param))
.self$sendBigData(fill_cmd)
.self$waitForImported()
}
}
}
)
NaviCell$methods(
sampleAnnotationSelectAnnotation = function(annotation_name, true_or_false) {
"Select or un-select an annotation for creating groups from a sample annotation table. true_or_false = TRUE, select, true_or_false = FALSE, un-select."
.self$incMessageId()
list_param <- list(module='', args = list("select_annotation", annotation_name, true_or_false), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
sampleAnnotationApply = function(...) {
"Apply the modifications done on a sample annotation table."
.self$incMessageId()
list_param <- list(module='', args = list("apply"), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
sampleAnnotationOpen = function(...) {
"Open sample annotation dialog."
.self$incMessageId()
list_param <- list(module='', args = list("open"), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
sampleAnnotationClose = function(...) {
"Close sample annotation dialog."
.self$incMessageId()
list_param <- list(module='', args = list("close"), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
NaviCell$methods(
sampleAnnotationCancel = function(...) {
"Cancel changes and close sample annotation dialog."
.self$incMessageId()
list_param <- list(module='', args = list("cancel"), msg_id = .self$msg_id, action = 'nv_sample_annotation_perform')
str_data <- .self$makeData(.self$formatJson(list_param))
.self$incMessageId()
response <- postForm(.self$proxy_url, style = 'POST', id = .self$session_id, msg_id = .self$msg_id, mode='cli2srv', perform='send_and_rcv', data=str_data, .opts=curlOptions(ssl.verifypeer=F))
#print(.self$formatResponse(response))
}
)
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