Nothing
################################################################################
### Aux functions
# generateReport
# argsList=
# parentWindow, statusbar,
# expressionText, comboExpressionPlot,
# commonFields$comboFeaTool, commonFields$feaResultsText,
# commonFields$thresholdAttributeNetworkText, commonFields$thresholdValueNetworkText, commonFields$thresholdOperatorNetworkText
# plotChecksValues
generateReport <- function(button, argsList) # button: Not used, but required for signalConnect.
{
data("FEA_tools", envir = environment())
FEA_tools<- get("FEA_tools", envir = environment())
inputFile <- argsList$commonFields$feaResultsText$getText()
reportTool <- argsList$commonFields$comboFeaTool$getActive()
reportTool <- rownames(FEA_tools)[which(as.numeric(FEA_tools[,"ID"])==reportTool)]
# Recargar siempre? donde poner para q solo cuando cambia?
feaResults <- readFEAresults(feaResultsText=argsList$commonFields$feaResultsText,comboFeaTool=argsList$commonFields$comboFeaTool, expressionText=argsList$commonFields$expressionText,
serverWebReportText=argsList$commonFields$serverWebReportText,alreadyDownloadedCheck=argsList$commonFields$alreadyDownloadedCheck, parentWindow=argsList$parentWindow)
if(is.null(feaResults) || (reportTool==-1 || inputFile==""))
{
# Dialog
dialog <- RGtk2::gtkDialogNewWithButtons("FEA results required", argsList$parentWindow,
c("modal", "destroy-with-parent"),
"gtk-ok", RGtk2::GtkResponseType["accept"],
show=TRUE)
dialog[["vbox"]]$add(RGtk2::gtkLabel("Please provide a file with FEA results to continue."))
response <- dialog$run()
dialog$destroy()
}else
{
if(grepl(".RData", inputFile, fixed=TRUE))
{
load(inputFile)
}
###################################################################
# Get arguments
# plotKeggPw <- argsList$plotChecksValues[["plotKeggPw"]]$active
plotGoTree <- argsList$plotChecksValues[["plotGoTree"]]$active
onlyGoLeaves <- argsList$plotChecksValues[["onlyGoLeaves"]]$active # Not for GtLinker. Only david (&other?)
geneExpr <- processExpressionField(argsList$commonFields$expressionText)
plotExpression <- names(argsList$commonFields$exprPlotOptionsID)[which(argsList$commonFields$exprPlotOptionsID==argsList$commonFields$comboExpressionPlot$getActive())]
filterAttribute <- argsList$commonFields$thresholdAttributeNetworkText$getText() # Only david and gTLinker
if(filterAttribute=="") filterAttribute <- NULL
filterThreshold <- argsList$commonFields$thresholdValueNetworkText$getText()
if(filterThreshold=="") filterThreshold <- 0
filterOperator <- argsList$commonFields$thresholdOperatorNetworkText$getText()
if(filterOperator=="") filterOperator <- NULL
# Report
argsList$statusbar$push(argsList$statusbar$getContextId("info"), "Generating report...")
tryCatch(
{
FGNet_report(feaResults, geneExpr=geneExpr, plotExpression=plotExpression, onlyGoLeaves=onlyGoLeaves, plotGoTree=plotGoTree,
filterAttribute=filterAttribute, filterOperator=filterOperator, filterThreshold=filterThreshold)
argsList$statusbar$push(argsList$statusbar$getContextId("info"), "Report ready.")
}, error = function (e)
{
argsList$statusbar$push(argsList$statusbar$getContextId("info"), "Error generating report. See R console for details.")
setwd("..")
stop(e)
})
}
}
#################################################################################
### Fills Report tab
#################################################################################
tabReport_fill <- function(mainWindow, statusbar, commonFields)
{
# report_david:
# geneLabels=NULL
tabReport <- RGtk2::gtkVBox(FALSE,3)
# plotChecks
plotChecks <- c("plotGoTree", "onlyGoLeaves") # onlyGoLeaves (only David/other?) TODO
plotChecksFrame <- RGtk2::gtkFrame("Plot options")
plotChecksArea <- RGtk2::gtkVBoxNew(homogeneous=FALSE, spacing=0)
plotChecksFrame$add(plotChecksArea)
plotChecksValues <-list()
for(ck in plotChecks)
{
plotChecksValues[[ck]] <- RGtk2::gtkCheckButton(ck)
plotChecksValues[[ck]]$active <- TRUE
plotChecksArea$add(plotChecksValues[[ck]])
}
tabReport$packStart(plotChecksFrame, expand=FALSE)
# Report tab end
buttonReport <- RGtk2::gtkButton("Create")
tabReport$packStart(buttonReport, expand = FALSE, FALSE, 10)
RGtk2::gSignalConnect(buttonReport, "clicked", generateReport, data=list(parentWindow=mainWindow, statusbar=statusbar,
commonFields=commonFields, plotChecksValues=plotChecksValues))
return(list(tabReport=tabReport, fields=list(plotChecksValues=plotChecksValues)))
}
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