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R/GUI_tabNetwork_tabOnlyNw.R
In FGNet: Functional Gene Networks derived from biological enrichment analyses
Defines functions
tabPlotNetwork_fill
generateNetwork
selectNetworkType
################################################################################
### Aux functions
# selectNetworkType
# generateNetwork
# argsList= comboFunNwIntNw, funNwIntNwID, plotTitleText, weightedCheck, keepAllNodesCheck, comboPlotOutput,plotOutputID
selectNetworkType <- function(aux, argsList)
{
selNwTypeID<- which(argsList$funNwIntNwID==argsList$comboFunNwIntNw$getActive())
selNwTypeTxt <- names(argsList$funNwIntNwText)[selNwTypeID]
if(names(selNwTypeID) %in% c("default","bipartite"))
{
argsList$plotTitleText$setText(selNwTypeTxt)
RGtk2::gtkWidgetSetSensitive(argsList$plotTitleText, TRUE)
RGtk2::gtkWidgetSetSensitive(argsList$comboPlotOutput, TRUE)
if(names(selNwTypeID) == "default")
{
RGtk2::gtkWidgetSetSensitive(argsList$weightedCheck, TRUE)
RGtk2::gtkWidgetSetSensitive(argsList$keepAllNodesCheck, FALSE)
}
if(names(selNwTypeID) == "bipartite")
{
RGtk2::gtkWidgetSetSensitive(argsList$weightedCheck, FALSE)
RGtk2::gtkWidgetSetSensitive(argsList$keepAllNodesCheck, TRUE)
}
}
if(names(selNwTypeID) == "both")
{
argsList$comboPlotOutput$setActive(argsList$plotOutputID["dynamic"])
RGtk2::gtkWidgetSetSensitive(argsList$comboPlotOutput, FALSE)
argsList$plotTitleText$setText("")
RGtk2::gtkWidgetSetSensitive(argsList$plotTitleText, FALSE)
RGtk2::gtkWidgetSetSensitive(argsList$weightedCheck, TRUE)
RGtk2::gtkWidgetSetSensitive(argsList$keepAllNodesCheck, TRUE)
}
}
# argsList=
# parentWindow, statusbar
# commonFields: feaResultsText, comboFeaTool, thresholdAttributeNetworkText, thresholdValueNetworkText, thresholdOperatorNetworkText, expressionText, comboExpressionPlot
# all tabPlotNetwork fields (onlyNwFields)
generateNetwork <- function(button, argsList) # button: Not used, but required for signalConnect.
{
data("FEA_tools", envir = environment())
FEA_tools<- get("FEA_tools", envir = environment())
###################################################################
# Start processing
inputFile <- argsList$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)
# inputFile is GTLinker jobID?
if(!is.na(suppressWarnings(as.numeric(inputFile)))) inputFile <- feaResults$fileName
if(is.null(feaResults) || (reportTool==-1 || inputFile==""))
{
# Dialog
dialog <- RGtk2::gtkDialogNewWithButtons("FEA results required", argsList$parentWindow,
c("modal", "destroy-with-parent"),
"gtk-ok", RGtk2::GtkResponseType["accept"],
show=TRUE)
dialog[["vbox"]]$add(RGtk2::gtkLabel("Please provide a file with the FEA results to continue."))
response <- dialog$run()
dialog$destroy()
}else
{
###################################################################
# Get arguments
geneExpr <- processExpressionField(argsList$commonFields$expressionText)
plotExpression <- names(argsList$commonFields$exprPlotOptionsID)[which(argsList$commonFields$exprPlotOptionsID==argsList$commonFields$comboExpressionPlot$getActive())]
###################################################################
# Go to the given file directory
folder <- strsplit(inputFile, .Platform$file.sep, fixed=TRUE)[[1]]
folder <- sub(folder[length(folder)],"",inputFile)
# Create folder
currWD <- getwd()
if(folder!="")
{
if((!file.exists(file.path(folder))))
{
dir.create(file.path(folder))
}
setwd(folder)
}
####################################
#### Plot networks
retFNw <- NULL
if(!is.null(feaResults))
{
argsList$statusbar$push(argsList$statusbar$getContextId("info"), "Generating network...")
# Subnetwork
if(button$label %in% c("nw1","nw2","nw3","nw5","nw6","nw7","nw8"))
{
# # Get selected cluster
# selCluster=""
# if(txtSelectCluster$visible) selCluster <- txtSelectCluster$getText()
# if(comboSelectCluster$visible) selCluster <- names(clustersId)[which(clustersId==comboSelectCluster$getActive())]
# if(selCluster=="") selCluster <- clustersId[1]
# txtSelectCluster$setText("")
#
# # Fill combo
# comboSelectCluster$getModel()$clear()
# for (i in names(clustersId)) RGtk2::gtkComboBoxAppendText(comboSelectCluster, i)
# comboSelectCluster$setActive(clustersId[selCluster])
# RGtk2::gtkWidgetSetSensitive(comboSelectCluster, TRUE)
# comboSelectCluster$Show()
# RGtk2::gtkWidgetSetSensitive(txtSelectCluster, FALSE)
# txtSelectCluster$Hide()
#
# subNwType <- button$label
# plotOutput <- names(argsList$onlyNwFields$plotOutputID)[which(argsList$onlyNwFields$plotOutputID==argsList$onlyNwFields$comboClplotOutput$getActive())] # "dinamic","static"
#
## add trycatch
# retFNw <- plotSubNetwork(feaResults, selCluster=selCluster, plotOutput=subNwType, plotOutput=plotOutput, returnGraph=saveCheck$active, geneExpr=geneExpr,plotExpression=plotExpression)
#
}else # FunctionalNetwork
{
jobName <- getJobName(feaResults$fileName) # for save
##############################
# Get arguments
# toMatrix():
key <- names(argsList$onlyNwFields$keysID)[which(argsList$onlyNwFields$keysID==argsList$onlyNwFields$comboKey$getActive())]
sepChar <- NULL
clusterColumn <- NULL
filterAttribute <- argsList$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
removeFiltered <- NULL
# functionalNetwork():
weighted <- argsList$onlyNwFields$weightedCheck$active
keepAllNodes <- argsList$onlyNwFields$keepAllNodesCheck$active
plotAllMg <- keepAllNodes
plotTitle <- argsList$onlyNwFields$plotTitleText$getText()
legendPrefix <- argsList$onlyNwFields$legendPrefixText$getText()
legendText <- NULL
if(!argsList$onlyNwFields$showLegendCheck$active) legendText <- FALSE
vSize <- as.numeric(argsList$onlyNwFields$vSizeText$getText())
vLabelCex <- as.numeric(argsList$onlyNwFields$vLabelCexText$getText())
bgTransparency <- as.numeric(argsList$onlyNwFields$bgTransparencyText$getText())
eColor <- argsList$onlyNwFields$eColorText$getText()
nwType <- names(argsList$onlyNwFields$funNwIntNwID)[which(argsList$onlyNwFields$funNwIntNwID==argsList$onlyNwFields$comboFunNwIntNw$getActive())] # "functionalNetwork","intersectionNetwork","both"
if(nwType=="both") nwType <- names(argsList$onlyNwFields$funNwIntNwID)[1:2]
plotOutput <- names(argsList$onlyNwFields$plotOutputID)[which(argsList$onlyNwFields$plotOutputID==argsList$onlyNwFields$comboPlotOutput$getActive())] # "dinamic","static"
#### PLOT
# Matrices
matr <- fea2incidMat(feaResults=feaResults, key=key, sepChar=sepChar, clusterColumn=clusterColumn, filterAttribute=filterAttribute, filterThreshold=filterThreshold,filterOperator=filterOperator, removeFilteredGtl=removeFiltered)
# Plot
retFNw <- tryCatch(
{
tmpReply <- functionalNetwork(matr, plotOutput=plotOutput, plotType=nwType,
plotTitle=plotTitle, legendPrefix=legendPrefix, legendText=legendText,
plotExpression=plotExpression,geneExpr=geneExpr,
vSize=vSize, vLabelCex=vLabelCex, eColor=eColor,
weighted=weighted, bgTransparency=bgTransparency,
plotTitleSub=NULL, keepAllNodes=keepAllNodes, plotAllMg=plotAllMg) # MISSING!!!
argsList$statusbar$push(argsList$statusbar$getContextId("info"), "Network ready.")
tmpReply # (invisible returns)
}, error = function(e)
{
argsList$statusbar$push(argsList$statusbar$getContextId("info"), "Error in network. See R console for details.")
stop(e)
})
}
####################################
# Save return
if(argsList$onlyNwFields$saveCheck$active)
{
if(jobName=="") jobName <- "network"
jobName <- paste(jobName,"_network.RData",sep="")
save(retFNw, file=jobName)
message(paste("Network saved as ",jobName, sep=""))
}
}
setwd(currWD)
}
}
#################################################################################
### Fills the Only network tab
#################################################################################
tabPlotNetwork_fill <- function(mainWindow, statusbar, commonFields)
{
tabPlotNetwork <- RGtk2::gtkVBox(FALSE,3)
### plotOptionsFrame
# Not added: sepChar, vLayout=NULL, keepColors=TRUE
plotOptionsExpander <- RGtk2::gtkExpanderNew("More options")
fgnPlotOptionsBox <- RGtk2::gtkVBox(FALSE,3)
fgnPlotOptionsL1Box <- RGtk2::gtkHBox(FALSE,3)
fgnPlotOptionsL2Box <- RGtk2::gtkHBox(FALSE,3)
fgnPlotOptionsL1bBox <- RGtk2::gtkHBox(FALSE,3)
fgnPlotOptionsL3Box <- RGtk2::gtkHBox(FALSE,3)
fgnPlotOptionsL4Box <- RGtk2::gtkHBox(FALSE,3)
fgnPlotOptionsL5Box <- RGtk2::gtkHBox(FALSE,3)
# key="Genes"
keysID <- setNames(0:1, c("Genes","Terms"))
comboKeyFrame <- RGtk2::gtkFrame("Network type")
RGtk2::gtkFrameSetShadowType(comboKeyFrame, GtkShadowType["none"])
comboKey <- RGtk2::gtkComboBoxNewText()
for (i in names(keysID)) RGtk2::gtkComboBoxAppendText(comboKey, i)
comboKey$setActive(keysID["Genes"])
comboKey$"tooltip-text" <- "Network nodes"
comboKeyFrame$add(comboKey)
fgnPlotOptionsL1Box$packStart(comboKeyFrame, expand=FALSE)
# plotFunctionalNetwork
funNwIntNwID <- setNames(0:2, c("default","bipartite","both"))
funNwIntNwText <- setNames(0:2, c("Functional Network (default)","Intersection Network (bipartite)","Both"))
funNwIntNwFrame <- RGtk2::gtkFrame("")
RGtk2::gtkFrameSetShadowType(funNwIntNwFrame, GtkShadowType["none"])
comboFunNwIntNw <- RGtk2::gtkComboBoxNewText()
for (i in names(funNwIntNwText)) RGtk2::gtkComboBoxAppendText(comboFunNwIntNw, i)
comboFunNwIntNw$setActive(funNwIntNwID["default"])
funNwIntNwFrame$add(comboFunNwIntNw)
fgnPlotOptionsL1Box$packStart(funNwIntNwFrame, expand=FALSE)
# plotOutput="static"
plotOutputID <- setNames(0:1, c("dynamic","static"))
plotOutputFrame <- RGtk2::gtkFrame("Output")
RGtk2::gtkFrameSetShadowType(plotOutputFrame, GtkShadowType["none"])
comboPlotOutput <- RGtk2::gtkComboBoxNewText()
for (i in capitalize(names(plotOutputID))) RGtk2::gtkComboBoxAppendText(comboPlotOutput, i)
comboPlotOutput$setActive(plotOutputID["static"])
comboPlotOutput$"tooltip-text" <- "static: standard R plot (R console) \ndynamic:interactive tkplot (metagroups background cannot be drawn)"
plotOutputFrame$add(comboPlotOutput)
fgnPlotOptionsL2Box$packStart(plotOutputFrame, expand=FALSE)
# Checkbox
fgnPlotOptionsHBox <- RGtk2::gtkHBox(FALSE,3)
# save
saveCheck<- RGtk2::gtkCheckButton("Save (.RData)")
saveCheck$"tooltip-text" <- "Save igraph & matrices"
fgnPlotOptionsL2Box$packStart(saveCheck, expand=FALSE)
# weighted=FALSE
weightedCheck<- RGtk2::gtkCheckButton("Weighted")
weightedCheck$"tooltip-text" <- "Edge width based on the number of shared gene-term sets"
fgnPlotOptionsHBox$packStart(weightedCheck, expand=FALSE)
# keepAllNodes=FALSE
keepAllNodesCheck<- RGtk2::gtkCheckButton("keepAllNodes")
keepAllNodesCheck$"tooltip-text" <- "Show all nodes, including those in only one cluster"
RGtk2::gtkWidgetSetSensitive(keepAllNodesCheck, FALSE)
fgnPlotOptionsHBox$packStart(keepAllNodesCheck, expand=FALSE)
fgnPlotOptionsL1bBox$packStart(fgnPlotOptionsHBox, expand=FALSE)
# plotTitle="Functional Network"
plotTitleFrame <- RGtk2::gtkFrame("Title")
RGtk2::gtkFrameSetShadowType(plotTitleFrame, GtkShadowType["none"])
plotTitleText <- RGtk2::gtkEntryNew()
plotTitleText$setWidthChars(15)
plotTitleText$setText("Functional Network")
plotTitleFrame$add(plotTitleText)
fgnPlotOptionsL3Box$packStart(plotTitleFrame, expand=TRUE)
# legendPrefix=NULL
legendPrefixFrame <- RGtk2::gtkFrame("Legend prefix")
legendPrefixBox <- RGtk2::gtkHBox(FALSE,3)
RGtk2::gtkFrameSetShadowType(legendPrefixFrame, GtkShadowType["none"])
legendPrefixText <- RGtk2::gtkEntryNew()
legendPrefixText$setText("Cl ")
legendPrefixText$setWidthChars(7)
legendPrefixBox$packStart(legendPrefixText, expand=FALSE)
showLegendCheck<- RGtk2::gtkCheckButton("Show legend")
showLegendCheck$active <- TRUE
legendPrefixBox$packStart(showLegendCheck, expand=FALSE)
legendPrefixFrame$add(legendPrefixBox)
fgnPlotOptionsL3Box$packStart(legendPrefixFrame, expand=FALSE)
# legendText=NULL
# vSize=12
vSizeFrame <- RGtk2::gtkFrame("vSize")
RGtk2::gtkFrameSetShadowType(vSizeFrame, GtkShadowType["none"])
vSizeText <- RGtk2::gtkEntryNew()
vSizeText$setWidthChars(5)
vSizeText$setText("12")
vSizeText$"tooltip-text" <- "Vertex (node) size"
vSizeFrame$add(vSizeText)
fgnPlotOptionsL4Box$packStart(vSizeFrame, expand=TRUE)
# vLabelCex=0.75
vLabelCexFrame <- RGtk2::gtkFrame("LabelCex")
RGtk2::gtkFrameSetShadowType(vLabelCexFrame, GtkShadowType["none"])
vLabelCexText <- RGtk2::gtkEntryNew()
vLabelCexText$setWidthChars(5)
vLabelCexText$setText("0.75")
vLabelCexText$"tooltip-text" <- "Node label size"
vLabelCexFrame$add(vLabelCexText)
fgnPlotOptionsL4Box$packStart(vLabelCexFrame, expand=TRUE)
# bgTransparency=0.4
bgTransparencyFrame <- RGtk2::gtkFrame("bgTransp.")
RGtk2::gtkFrameSetShadowType(bgTransparencyFrame, GtkShadowType["none"])
bgTransparencyText <- RGtk2::gtkEntryNew()
bgTransparencyText$"tooltip-text" <- "Background transparency"
bgTransparencyText$setWidthChars(5)
bgTransparencyText$setText("0.4")
bgTransparencyFrame$add(bgTransparencyText)
fgnPlotOptionsL4Box$packStart(bgTransparencyFrame, expand=TRUE)
# eColor="#323232"
eColorFrame <- RGtk2::gtkFrame("eColor")
RGtk2::gtkFrameSetShadowType(eColorFrame, GtkShadowType["none"])
eColorText <- RGtk2::gtkEntryNew()
bgTransparencyText$setWidthChars(5)
eColorText$setText("#323232")
eColorText$"tooltip-text" <- "Edge color"
eColorFrame$add(eColorText)
fgnPlotOptionsL4Box$packStart(eColorFrame, expand=FALSE)
# Tab end
fgnPlotOptionsBox$packStart(fgnPlotOptionsL3Box, expand=FALSE,10)
fgnPlotOptionsBox$packStart(fgnPlotOptionsL4Box, expand=FALSE,10)
fgnPlotOptionsBox$packStart(fgnPlotOptionsL5Box, expand=FALSE,10)
plotOptionsExpander$add(fgnPlotOptionsBox)
tabPlotNetwork$packStart(fgnPlotOptionsL1Box, expand=FALSE,10)
tabPlotNetwork$packStart(fgnPlotOptionsL1bBox, expand=FALSE,10)
tabPlotNetwork$packStart(fgnPlotOptionsL2Box, expand=FALSE,10)
tabPlotNetwork$packStart(plotOptionsExpander, expand=FALSE,10)
buttonNetwork <- RGtk2::gtkButton("Create")
tabPlotNetwork$packStart(buttonNetwork, expand = FALSE, FALSE, 10)
# Make list with fields:
fields <- list(comboKey=comboKey,keysID=keysID, comboFunNwIntNw=comboFunNwIntNw, funNwIntNwID=funNwIntNwID, funNwIntNwText=funNwIntNwText, weightedCheck=weightedCheck, keepAllNodesCheck=keepAllNodesCheck, comboPlotOutput=comboPlotOutput,plotOutputID=plotOutputID, saveCheck=saveCheck,
plotTitleText=plotTitleText, legendPrefixText=legendPrefixText, showLegendCheck=showLegendCheck,
vSizeText=vSizeText, vLabelCexText=vLabelCexText, bgTransparencyText=bgTransparencyText, eColorText=eColorText)
# SignalConnects
RGtk2::gSignalConnect(buttonNetwork, "clicked", generateNetwork, data=list(parentWindow=mainWindow, statusbar=statusbar,
commonFields=commonFields, onlyNwFields=fields))
RGtk2::gSignalConnect(comboFunNwIntNw, "changed", selectNetworkType, data=list(comboFunNwIntNw=comboFunNwIntNw,funNwIntNwID=funNwIntNwID, funNwIntNwText=funNwIntNwText, plotTitleText=plotTitleText, comboPlotOutput=comboPlotOutput,plotOutputID=plotOutputID,
weightedCheck=weightedCheck, keepAllNodesCheck=keepAllNodesCheck))
return(list(tabPlotNetwork=tabPlotNetwork, fields=fields))
}
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Defines functions tabPlotNetwork_fill generateNetwork selectNetworkType
################################################################################
### Aux functions
# selectNetworkType
# generateNetwork
# argsList= comboFunNwIntNw, funNwIntNwID, plotTitleText, weightedCheck, keepAllNodesCheck, comboPlotOutput,plotOutputID
selectNetworkType <- function(aux, argsList)
{
selNwTypeID<- which(argsList$funNwIntNwID==argsList$comboFunNwIntNw$getActive())
selNwTypeTxt <- names(argsList$funNwIntNwText)[selNwTypeID]
if(names(selNwTypeID) %in% c("default","bipartite"))
{
argsList$plotTitleText$setText(selNwTypeTxt)
RGtk2::gtkWidgetSetSensitive(argsList$plotTitleText, TRUE)
RGtk2::gtkWidgetSetSensitive(argsList$comboPlotOutput, TRUE)
if(names(selNwTypeID) == "default")
{
RGtk2::gtkWidgetSetSensitive(argsList$weightedCheck, TRUE)
RGtk2::gtkWidgetSetSensitive(argsList$keepAllNodesCheck, FALSE)
}
if(names(selNwTypeID) == "bipartite")
{
RGtk2::gtkWidgetSetSensitive(argsList$weightedCheck, FALSE)
RGtk2::gtkWidgetSetSensitive(argsList$keepAllNodesCheck, TRUE)
}
}
if(names(selNwTypeID) == "both")
{
argsList$comboPlotOutput$setActive(argsList$plotOutputID["dynamic"])
RGtk2::gtkWidgetSetSensitive(argsList$comboPlotOutput, FALSE)
argsList$plotTitleText$setText("")
RGtk2::gtkWidgetSetSensitive(argsList$plotTitleText, FALSE)
RGtk2::gtkWidgetSetSensitive(argsList$weightedCheck, TRUE)
RGtk2::gtkWidgetSetSensitive(argsList$keepAllNodesCheck, TRUE)
}
}
# argsList=
# parentWindow, statusbar
# commonFields: feaResultsText, comboFeaTool, thresholdAttributeNetworkText, thresholdValueNetworkText, thresholdOperatorNetworkText, expressionText, comboExpressionPlot
# all tabPlotNetwork fields (onlyNwFields)
generateNetwork <- function(button, argsList) # button: Not used, but required for signalConnect.
{
data("FEA_tools", envir = environment())
FEA_tools<- get("FEA_tools", envir = environment())
###################################################################
# Start processing
inputFile <- argsList$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)
# inputFile is GTLinker jobID?
if(!is.na(suppressWarnings(as.numeric(inputFile)))) inputFile <- feaResults$fileName
if(is.null(feaResults) || (reportTool==-1 || inputFile==""))
{
# Dialog
dialog <- RGtk2::gtkDialogNewWithButtons("FEA results required", argsList$parentWindow,
c("modal", "destroy-with-parent"),
"gtk-ok", RGtk2::GtkResponseType["accept"],
show=TRUE)
dialog[["vbox"]]$add(RGtk2::gtkLabel("Please provide a file with the FEA results to continue."))
response <- dialog$run()
dialog$destroy()
}else
{
###################################################################
# Get arguments
geneExpr <- processExpressionField(argsList$commonFields$expressionText)
plotExpression <- names(argsList$commonFields$exprPlotOptionsID)[which(argsList$commonFields$exprPlotOptionsID==argsList$commonFields$comboExpressionPlot$getActive())]
###################################################################
# Go to the given file directory
folder <- strsplit(inputFile, .Platform$file.sep, fixed=TRUE)[[1]]
folder <- sub(folder[length(folder)],"",inputFile)
# Create folder
currWD <- getwd()
if(folder!="")
{
if((!file.exists(file.path(folder))))
{
dir.create(file.path(folder))
}
setwd(folder)
}
####################################
#### Plot networks
retFNw <- NULL
if(!is.null(feaResults))
{
argsList$statusbar$push(argsList$statusbar$getContextId("info"), "Generating network...")
# Subnetwork
if(button$label %in% c("nw1","nw2","nw3","nw5","nw6","nw7","nw8"))
{
# # Get selected cluster
# selCluster=""
# if(txtSelectCluster$visible) selCluster <- txtSelectCluster$getText()
# if(comboSelectCluster$visible) selCluster <- names(clustersId)[which(clustersId==comboSelectCluster$getActive())]
# if(selCluster=="") selCluster <- clustersId[1]
# txtSelectCluster$setText("")
#
# # Fill combo
# comboSelectCluster$getModel()$clear()
# for (i in names(clustersId)) RGtk2::gtkComboBoxAppendText(comboSelectCluster, i)
# comboSelectCluster$setActive(clustersId[selCluster])
# RGtk2::gtkWidgetSetSensitive(comboSelectCluster, TRUE)
# comboSelectCluster$Show()
# RGtk2::gtkWidgetSetSensitive(txtSelectCluster, FALSE)
# txtSelectCluster$Hide()
#
# subNwType <- button$label
# plotOutput <- names(argsList$onlyNwFields$plotOutputID)[which(argsList$onlyNwFields$plotOutputID==argsList$onlyNwFields$comboClplotOutput$getActive())] # "dinamic","static"
#
## add trycatch
# retFNw <- plotSubNetwork(feaResults, selCluster=selCluster, plotOutput=subNwType, plotOutput=plotOutput, returnGraph=saveCheck$active, geneExpr=geneExpr,plotExpression=plotExpression)
#
}else # FunctionalNetwork
{
jobName <- getJobName(feaResults$fileName) # for save
##############################
# Get arguments
# toMatrix():
key <- names(argsList$onlyNwFields$keysID)[which(argsList$onlyNwFields$keysID==argsList$onlyNwFields$comboKey$getActive())]
sepChar <- NULL
clusterColumn <- NULL
filterAttribute <- argsList$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
removeFiltered <- NULL
# functionalNetwork():
weighted <- argsList$onlyNwFields$weightedCheck$active
keepAllNodes <- argsList$onlyNwFields$keepAllNodesCheck$active
plotAllMg <- keepAllNodes
plotTitle <- argsList$onlyNwFields$plotTitleText$getText()
legendPrefix <- argsList$onlyNwFields$legendPrefixText$getText()
legendText <- NULL
if(!argsList$onlyNwFields$showLegendCheck$active) legendText <- FALSE
vSize <- as.numeric(argsList$onlyNwFields$vSizeText$getText())
vLabelCex <- as.numeric(argsList$onlyNwFields$vLabelCexText$getText())
bgTransparency <- as.numeric(argsList$onlyNwFields$bgTransparencyText$getText())
eColor <- argsList$onlyNwFields$eColorText$getText()
nwType <- names(argsList$onlyNwFields$funNwIntNwID)[which(argsList$onlyNwFields$funNwIntNwID==argsList$onlyNwFields$comboFunNwIntNw$getActive())] # "functionalNetwork","intersectionNetwork","both"
if(nwType=="both") nwType <- names(argsList$onlyNwFields$funNwIntNwID)[1:2]
plotOutput <- names(argsList$onlyNwFields$plotOutputID)[which(argsList$onlyNwFields$plotOutputID==argsList$onlyNwFields$comboPlotOutput$getActive())] # "dinamic","static"
#### PLOT
# Matrices
matr <- fea2incidMat(feaResults=feaResults, key=key, sepChar=sepChar, clusterColumn=clusterColumn, filterAttribute=filterAttribute, filterThreshold=filterThreshold,filterOperator=filterOperator, removeFilteredGtl=removeFiltered)
# Plot
retFNw <- tryCatch(
{
tmpReply <- functionalNetwork(matr, plotOutput=plotOutput, plotType=nwType,
plotTitle=plotTitle, legendPrefix=legendPrefix, legendText=legendText,
plotExpression=plotExpression,geneExpr=geneExpr,
vSize=vSize, vLabelCex=vLabelCex, eColor=eColor,
weighted=weighted, bgTransparency=bgTransparency,
plotTitleSub=NULL, keepAllNodes=keepAllNodes, plotAllMg=plotAllMg) # MISSING!!!
argsList$statusbar$push(argsList$statusbar$getContextId("info"), "Network ready.")
tmpReply # (invisible returns)
}, error = function(e)
{
argsList$statusbar$push(argsList$statusbar$getContextId("info"), "Error in network. See R console for details.")
stop(e)
})
}
####################################
# Save return
if(argsList$onlyNwFields$saveCheck$active)
{
if(jobName=="") jobName <- "network"
jobName <- paste(jobName,"_network.RData",sep="")
save(retFNw, file=jobName)
message(paste("Network saved as ",jobName, sep=""))
}
}
setwd(currWD)
}
}
#################################################################################
### Fills the Only network tab
#################################################################################
tabPlotNetwork_fill <- function(mainWindow, statusbar, commonFields)
{
tabPlotNetwork <- RGtk2::gtkVBox(FALSE,3)
### plotOptionsFrame
# Not added: sepChar, vLayout=NULL, keepColors=TRUE
plotOptionsExpander <- RGtk2::gtkExpanderNew("More options")
fgnPlotOptionsBox <- RGtk2::gtkVBox(FALSE,3)
fgnPlotOptionsL1Box <- RGtk2::gtkHBox(FALSE,3)
fgnPlotOptionsL2Box <- RGtk2::gtkHBox(FALSE,3)
fgnPlotOptionsL1bBox <- RGtk2::gtkHBox(FALSE,3)
fgnPlotOptionsL3Box <- RGtk2::gtkHBox(FALSE,3)
fgnPlotOptionsL4Box <- RGtk2::gtkHBox(FALSE,3)
fgnPlotOptionsL5Box <- RGtk2::gtkHBox(FALSE,3)
# key="Genes"
keysID <- setNames(0:1, c("Genes","Terms"))
comboKeyFrame <- RGtk2::gtkFrame("Network type")
RGtk2::gtkFrameSetShadowType(comboKeyFrame, GtkShadowType["none"])
comboKey <- RGtk2::gtkComboBoxNewText()
for (i in names(keysID)) RGtk2::gtkComboBoxAppendText(comboKey, i)
comboKey$setActive(keysID["Genes"])
comboKey$"tooltip-text" <- "Network nodes"
comboKeyFrame$add(comboKey)
fgnPlotOptionsL1Box$packStart(comboKeyFrame, expand=FALSE)
# plotFunctionalNetwork
funNwIntNwID <- setNames(0:2, c("default","bipartite","both"))
funNwIntNwText <- setNames(0:2, c("Functional Network (default)","Intersection Network (bipartite)","Both"))
funNwIntNwFrame <- RGtk2::gtkFrame("")
RGtk2::gtkFrameSetShadowType(funNwIntNwFrame, GtkShadowType["none"])
comboFunNwIntNw <- RGtk2::gtkComboBoxNewText()
for (i in names(funNwIntNwText)) RGtk2::gtkComboBoxAppendText(comboFunNwIntNw, i)
comboFunNwIntNw$setActive(funNwIntNwID["default"])
funNwIntNwFrame$add(comboFunNwIntNw)
fgnPlotOptionsL1Box$packStart(funNwIntNwFrame, expand=FALSE)
# plotOutput="static"
plotOutputID <- setNames(0:1, c("dynamic","static"))
plotOutputFrame <- RGtk2::gtkFrame("Output")
RGtk2::gtkFrameSetShadowType(plotOutputFrame, GtkShadowType["none"])
comboPlotOutput <- RGtk2::gtkComboBoxNewText()
for (i in capitalize(names(plotOutputID))) RGtk2::gtkComboBoxAppendText(comboPlotOutput, i)
comboPlotOutput$setActive(plotOutputID["static"])
comboPlotOutput$"tooltip-text" <- "static: standard R plot (R console) \ndynamic:interactive tkplot (metagroups background cannot be drawn)"
plotOutputFrame$add(comboPlotOutput)
fgnPlotOptionsL2Box$packStart(plotOutputFrame, expand=FALSE)
# Checkbox
fgnPlotOptionsHBox <- RGtk2::gtkHBox(FALSE,3)
# save
saveCheck<- RGtk2::gtkCheckButton("Save (.RData)")
saveCheck$"tooltip-text" <- "Save igraph & matrices"
fgnPlotOptionsL2Box$packStart(saveCheck, expand=FALSE)
# weighted=FALSE
weightedCheck<- RGtk2::gtkCheckButton("Weighted")
weightedCheck$"tooltip-text" <- "Edge width based on the number of shared gene-term sets"
fgnPlotOptionsHBox$packStart(weightedCheck, expand=FALSE)
# keepAllNodes=FALSE
keepAllNodesCheck<- RGtk2::gtkCheckButton("keepAllNodes")
keepAllNodesCheck$"tooltip-text" <- "Show all nodes, including those in only one cluster"
RGtk2::gtkWidgetSetSensitive(keepAllNodesCheck, FALSE)
fgnPlotOptionsHBox$packStart(keepAllNodesCheck, expand=FALSE)
fgnPlotOptionsL1bBox$packStart(fgnPlotOptionsHBox, expand=FALSE)
# plotTitle="Functional Network"
plotTitleFrame <- RGtk2::gtkFrame("Title")
RGtk2::gtkFrameSetShadowType(plotTitleFrame, GtkShadowType["none"])
plotTitleText <- RGtk2::gtkEntryNew()
plotTitleText$setWidthChars(15)
plotTitleText$setText("Functional Network")
plotTitleFrame$add(plotTitleText)
fgnPlotOptionsL3Box$packStart(plotTitleFrame, expand=TRUE)
# legendPrefix=NULL
legendPrefixFrame <- RGtk2::gtkFrame("Legend prefix")
legendPrefixBox <- RGtk2::gtkHBox(FALSE,3)
RGtk2::gtkFrameSetShadowType(legendPrefixFrame, GtkShadowType["none"])
legendPrefixText <- RGtk2::gtkEntryNew()
legendPrefixText$setText("Cl ")
legendPrefixText$setWidthChars(7)
legendPrefixBox$packStart(legendPrefixText, expand=FALSE)
showLegendCheck<- RGtk2::gtkCheckButton("Show legend")
showLegendCheck$active <- TRUE
legendPrefixBox$packStart(showLegendCheck, expand=FALSE)
legendPrefixFrame$add(legendPrefixBox)
fgnPlotOptionsL3Box$packStart(legendPrefixFrame, expand=FALSE)
# legendText=NULL
# vSize=12
vSizeFrame <- RGtk2::gtkFrame("vSize")
RGtk2::gtkFrameSetShadowType(vSizeFrame, GtkShadowType["none"])
vSizeText <- RGtk2::gtkEntryNew()
vSizeText$setWidthChars(5)
vSizeText$setText("12")
vSizeText$"tooltip-text" <- "Vertex (node) size"
vSizeFrame$add(vSizeText)
fgnPlotOptionsL4Box$packStart(vSizeFrame, expand=TRUE)
# vLabelCex=0.75
vLabelCexFrame <- RGtk2::gtkFrame("LabelCex")
RGtk2::gtkFrameSetShadowType(vLabelCexFrame, GtkShadowType["none"])
vLabelCexText <- RGtk2::gtkEntryNew()
vLabelCexText$setWidthChars(5)
vLabelCexText$setText("0.75")
vLabelCexText$"tooltip-text" <- "Node label size"
vLabelCexFrame$add(vLabelCexText)
fgnPlotOptionsL4Box$packStart(vLabelCexFrame, expand=TRUE)
# bgTransparency=0.4
bgTransparencyFrame <- RGtk2::gtkFrame("bgTransp.")
RGtk2::gtkFrameSetShadowType(bgTransparencyFrame, GtkShadowType["none"])
bgTransparencyText <- RGtk2::gtkEntryNew()
bgTransparencyText$"tooltip-text" <- "Background transparency"
bgTransparencyText$setWidthChars(5)
bgTransparencyText$setText("0.4")
bgTransparencyFrame$add(bgTransparencyText)
fgnPlotOptionsL4Box$packStart(bgTransparencyFrame, expand=TRUE)
# eColor="#323232"
eColorFrame <- RGtk2::gtkFrame("eColor")
RGtk2::gtkFrameSetShadowType(eColorFrame, GtkShadowType["none"])
eColorText <- RGtk2::gtkEntryNew()
bgTransparencyText$setWidthChars(5)
eColorText$setText("#323232")
eColorText$"tooltip-text" <- "Edge color"
eColorFrame$add(eColorText)
fgnPlotOptionsL4Box$packStart(eColorFrame, expand=FALSE)
# Tab end
fgnPlotOptionsBox$packStart(fgnPlotOptionsL3Box, expand=FALSE,10)
fgnPlotOptionsBox$packStart(fgnPlotOptionsL4Box, expand=FALSE,10)
fgnPlotOptionsBox$packStart(fgnPlotOptionsL5Box, expand=FALSE,10)
plotOptionsExpander$add(fgnPlotOptionsBox)
tabPlotNetwork$packStart(fgnPlotOptionsL1Box, expand=FALSE,10)
tabPlotNetwork$packStart(fgnPlotOptionsL1bBox, expand=FALSE,10)
tabPlotNetwork$packStart(fgnPlotOptionsL2Box, expand=FALSE,10)
tabPlotNetwork$packStart(plotOptionsExpander, expand=FALSE,10)
buttonNetwork <- RGtk2::gtkButton("Create")
tabPlotNetwork$packStart(buttonNetwork, expand = FALSE, FALSE, 10)
# Make list with fields:
fields <- list(comboKey=comboKey,keysID=keysID, comboFunNwIntNw=comboFunNwIntNw, funNwIntNwID=funNwIntNwID, funNwIntNwText=funNwIntNwText, weightedCheck=weightedCheck, keepAllNodesCheck=keepAllNodesCheck, comboPlotOutput=comboPlotOutput,plotOutputID=plotOutputID, saveCheck=saveCheck,
plotTitleText=plotTitleText, legendPrefixText=legendPrefixText, showLegendCheck=showLegendCheck,
vSizeText=vSizeText, vLabelCexText=vLabelCexText, bgTransparencyText=bgTransparencyText, eColorText=eColorText)
# SignalConnects
RGtk2::gSignalConnect(buttonNetwork, "clicked", generateNetwork, data=list(parentWindow=mainWindow, statusbar=statusbar,
commonFields=commonFields, onlyNwFields=fields))
RGtk2::gSignalConnect(comboFunNwIntNw, "changed", selectNetworkType, data=list(comboFunNwIntNw=comboFunNwIntNw,funNwIntNwID=funNwIntNwID, funNwIntNwText=funNwIntNwText, plotTitleText=plotTitleText, comboPlotOutput=comboPlotOutput,plotOutputID=plotOutputID,
weightedCheck=weightedCheck, keepAllNodesCheck=keepAllNodesCheck))
return(list(tabPlotNetwork=tabPlotNetwork, fields=fields))
}
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