Nothing
#################################################################################
### Fills the common arguments
#################################################################################
tabNetwork_common_fill <- function(mainWindow,geneList)
{
tabNetwork <- RGtk2::gtkHBox(FALSE,3)
############################################################################
##### 1. Genes EXPRESSION text field
# Expression
table.Left <- RGtk2::gtkTable(rows=20,columns=2)
frameExpressionFields <- RGtk2::gtkFrame("Expression (only for ploting)")
RGtk2::gtkFrameSetShadowType(frameExpressionFields, GtkShadowType["none"])
table.Left$attach(frameExpressionFields, left.attach = 0,2, top.attach = 0,19, xoptions = c("expand", "fill"), yoptions = c("expand", "fill"))
tabNetwork$packStart(table.Left, TRUE, TRUE, 10)
# Scrolled area:
expressionArea <- RGtk2::gtkScrolledWindow()
expressionArea$setPolicy("automatic", "automatic")
expressionArea$setShadowType("in")
frameExpressionFields$add(expressionArea)
# Text field
expressionText <- RGtk2::gtkTextViewNewWithBuffer()
expressionText$grabFocus()
expressionText$"tooltip-text" <- "One gene per line, followed by its expression separated by tab or space"
expressionText$modifyFont(pangoFontDescriptionFromString(", monospace"))
expressionArea$add(expressionText)
# Add genes from argument to field
if(!is.null(geneList) && !is.null(names(geneList)))
{
genesBuffer <- RGtk2::gtkTextBufferNew()
RGtk2::gtkTextBufferSetText(genesBuffer,paste(paste(names(geneList), geneList,sep="\t"),collapse="\n"))
RGtk2::gtkTextViewSetBuffer(expressionText, genesBuffer)
}
# Combo
exprPlotOptionsID <- setNames(0:1, c("border","fill"))
exprPlotOptionsShow <- setNames(0:1, c("Border","Fill node"))
frameExpressionPlot <- RGtk2::gtkFrame("Plot as")
RGtk2::gtkFrameSetShadowType(frameExpressionPlot, GtkShadowType["none"])
comboExpressionPlot <- RGtk2::gtkComboBoxNewText()
for (i in capitalize(names(exprPlotOptionsShow))) RGtk2::gtkComboBoxAppendText(comboExpressionPlot, i)
RGtk2::gtkComboBoxSetTitle(comboExpressionPlot, "comboExpressionPlot")
comboExpressionPlot$setActive(exprPlotOptionsID["border"])
comboExpressionPlot$"tooltip-text" <- "Genes with positive values are plotted RED, negative values GREEN"
frameExpressionPlot$add(comboExpressionPlot)
table.Left$attach(frameExpressionPlot, left.attach = 0,1, top.attach = 19,20, xoptions = "", yoptions = "")
frameButtonSelectExprFile <- RGtk2::gtkFrameNew("")
RGtk2::gtkFrameSetShadowType(frameButtonSelectExprFile, GtkShadowType["none"])
buttonSelectExprFile <- RGtk2::gtkButton("Load from file") #.RData containing vector or .csv???
buttonSelectExprFile$"tooltip-text" <- "Text file with one gene per line, followed by its expression separated by TAB"
buttonSelectExprFile$name <- "buttonSelectExprFile"
gSignalConnect(buttonSelectExprFile, "clicked", loadFileDialog, data=list(parentWindow=mainWindow, expressionText=expressionText))
frameButtonSelectExprFile$add(buttonSelectExprFile)
table.Left$attach(frameButtonSelectExprFile, left.attach = 1,2, top.attach = 19,20, xoptions = "", yoptions = "")
############################################################################
##### 2. FGNet options
box.Right <- RGtk2::gtkVBoxNew(FALSE, 10)
frame.FGNetOptions <- RGtk2::gtkFrameNew("Functional Network")
#RGtk2::gtkFrameSetShadowType(frame.FGNetOptions, GtkShadowType["none"])
box.Right$add(frame.FGNetOptions)
tabNetwork$add(box.Right)
##### TOP (common box)
commonBox <- RGtk2::gtkVBoxNew(FALSE, 10)
commonBox$setBorderWidth(10)
fgnCommon1Box <- RGtk2::gtkHBox(FALSE,3)
### Tool
frameFeaTool <- RGtk2::gtkFrame("FEA tool")
RGtk2::gtkFrameSetShadowType(frameFeaTool, GtkShadowType["none"])
frameFeaTool2 <- RGtk2::gtkFrame("")
RGtk2::gtkFrameSetShadowType(frameFeaTool2, GtkShadowType["none"])
comboFeaTool <- RGtk2::gtkComboBoxNewText()
data("FEA_tools", envir = environment())
FEA_tools<- get("FEA_tools", envir = environment())
for (i in rownames(FEA_tools)) RGtk2::gtkComboBoxAppendText(comboFeaTool, i)
RGtk2::gtkComboBoxSetTitle(comboFeaTool, "comboFeaTool")
comboFeaTool$setActive(FEA_tools["Imported text file","ID"])
frameFeaTool$add(comboFeaTool)
fgnCommon1Box$packStart(frameFeaTool, expand=FALSE)
# Result
frameFEAresultsText <- RGtk2::gtkFrame("FEA results")
RGtk2::gtkFrameSetShadowType(frameFEAresultsText, GtkShadowType["none"])
feaResultsText <- RGtk2::gtkEntryNew()
#feaResultsText$setWidthChars(25)
frameFEAresultsText$add(feaResultsText)
fgnCommon1Box$packStart(frameFEAresultsText, expand=TRUE)
#gSignalConnect(feaResultsText, "changed", loadFEAresults?)
# Button
frameFEAfile <- RGtk2::gtkFrame("")
RGtk2::gtkFrameSetShadowType(frameFEAfile, GtkShadowType["none"])
buttonSelectFeaResults <- RGtk2::gtkButton("Select file")
buttonSelectFeaResults$name <- "buttonSelectFeaResults"
frameFEAfile$add(buttonSelectFeaResults)
fgnCommon1Box$packStart(frameFEAfile, expand=FALSE)
commonBox$packStart(fgnCommon1Box, expand=FALSE)
### GeneTerm Linker:
gtLinkerDownloadExpander <- RGtk2::gtkExpander("GeneTerm Linker download options", show=FALSE)
gtLinkerDownloadExpander$Hide()
gtLinkerDownloadBox <- RGtk2::gtkHBox(FALSE,3)
# Server
serverWebReportFrame <- RGtk2::gtkFrame("Server")
RGtk2::gtkFrameSetShadowType(serverWebReportFrame, GtkShadowType["none"])
serverWebReportText <- RGtk2::gtkEntryNew()
serverWebReportText$setWidthChars(25)
serverWebReportText$setText("http://gtlinker.cnb.csic.es")
serverWebReportFrame$add(serverWebReportText)
gtLinkerDownloadBox$packStart(serverWebReportFrame, expand=FALSE)
# Checkbox
alreadyDownloadedCheckFrame <- RGtk2::gtkFrame("")
RGtk2::gtkFrameSetShadowType(alreadyDownloadedCheckFrame, GtkShadowType["none"])
alreadyDownloadedCheck<- RGtk2::gtkCheckButton("AlreadyDownloaded")
alreadyDownloadedCheckFrame$add(alreadyDownloadedCheck)
gtLinkerDownloadBox$packStart(alreadyDownloadedCheckFrame, expand=FALSE)
# Add
gtLinkerDownloadExpander$add(gtLinkerDownloadBox)
RGtk2::gtkWidgetSetSensitive(gtLinkerDownloadExpander, FALSE)
gtLinkerDownloadExpander$Hide()
commonBox$packStart(gtLinkerDownloadExpander, expand=FALSE)
fgnCommon2Box <- RGtk2::gtkHBox(FALSE,3)
### Threshold frame
thresholdFrame <- RGtk2::gtkFrame("Filter clusters") # MG: silhouette, CL... # OTHER: TODO (desactivar si no es david/gtlinker?)
thresholdFrame$"tooltip-text" <- "Clusters that meet these criteria will be REMOVED from the network"
thresholdBoxNetwork <- RGtk2::gtkHBox(FALSE,3)
thresholdAttributeNetworkFrame <- RGtk2::gtkFrame("Attribute")
RGtk2::gtkFrameSetShadowType(thresholdAttributeNetworkFrame, GtkShadowType["none"])
thresholdAttributeNetworkText <- RGtk2::gtkEntryNew()
thresholdAttributeNetworkText$setWidthChars(15)
thresholdAttributeNetworkText$setText("")
thresholdAttributeNetworkFrame$add(thresholdAttributeNetworkText)
thresholdBoxNetwork$packStart(thresholdAttributeNetworkFrame, expand=TRUE,10)
thresholdOperatorNetworkFrame <- RGtk2::gtkFrame("Operator")
RGtk2::gtkFrameSetShadowType(thresholdOperatorNetworkFrame, GtkShadowType["none"])
thresholdOperatorNetworkText <- RGtk2::gtkEntryNew()
thresholdOperatorNetworkText$setWidthChars(5)
thresholdOperatorNetworkText$setText("<")
thresholdOperatorNetworkFrame$add(thresholdOperatorNetworkText)
thresholdBoxNetwork$packStart(thresholdOperatorNetworkFrame, expand=FALSE,10)
thresholdValueNetworkFrame <- RGtk2::gtkFrame("Value")
RGtk2::gtkFrameSetShadowType(thresholdValueNetworkFrame, GtkShadowType["none"])
thresholdValueNetworkText <- RGtk2::gtkEntryNew()
thresholdValueNetworkText$setWidthChars(5)
thresholdValueNetworkText$setText("0")
thresholdValueNetworkFrame$add(thresholdValueNetworkText)
thresholdBoxNetwork$packStart(thresholdValueNetworkFrame, expand=FALSE,10)
thresholdFrame$add(thresholdBoxNetwork)
fgnCommon2Box$packStart(thresholdFrame, expand=TRUE)
commonBox$packStart(fgnCommon2Box, expand=FALSE)
frame.FGNetOptions$add(commonBox)
# List fields:
fields <- list(expressionText=expressionText, comboExpressionPlot=comboExpressionPlot, exprPlotOptionsID=exprPlotOptionsID, buttonSelectExprFile=buttonSelectExprFile,
commonBox=commonBox,
comboFeaTool=comboFeaTool, frameFEAresultsText=frameFEAresultsText, feaResultsText=feaResultsText,
serverWebReportText=serverWebReportText,alreadyDownloadedCheck=alreadyDownloadedCheck,
thresholdFrame=thresholdFrame, thresholdAttributeNetworkText=thresholdAttributeNetworkText,
thresholdOperatorNetworkText=thresholdOperatorNetworkText, thresholdValueNetworkText=thresholdValueNetworkText,
gtLinkerDownloadExpander=gtLinkerDownloadExpander, buttonSelectFeaResults=buttonSelectFeaResults)
return(list(tabNetwork=tabNetwork, fields=fields))
}
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