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# exploRase - explorartory analysis of systems biology data
# exploRase code naming conventions:
# All functions and GUI objects will be in camelBackCase.
# All other variables are lower_case_underscore_delimited
# Public "API" functions are prefixed by 'exp_'
# All callback functions are postfixed with '_cb'
# Always keep the 'R' in exploRase lower-case in the code
# FYI:
# All global variables are stored in the '.exp' local namespace
# Start exploRase
# The main function of exploRase, normally invoked without arguments, unless
# one already has data/metadata in the R session to load
#
# @arguments Experimental data to load
# @arguments Entity metadata to load
# @arguments Experimental design information to load
# @arguments The entity type of the data being loaded
# @arguments A Bioconductor "graph" to load (not yet implemented)
# @arguments A list of entity lists to load
# @arguments The GGobi session to use
# @arguments Whether R should quit when exploRase is exited
# @keyword dynamic
explorase <-
function (exp_data = NULL, entity_info = NULL, design_info = NULL, type = "gene",
network = NULL, entity_lists = NULL, gobi = ggobi_get(), quit_on_exit = F)
{
#### Reset exploRase ####
if (exp_isRunning())
getMainWindow()$destroy() # kill existing exploRase, if any
.exp$clear() # ensure previous state is cleared
#### Initialize GGobi ####
if (!is.null(gobi))
gg <- gobi
else gg <- ggobi()
.exp$setGGobi(gg)
# FIXME: we need to be able update this on the fly from GGobi
.exp$setGGobiColors(toGdkColors(colorscheme(gg)$colors))
#### Initialize exploRase GUI ####
# disable animations (requires GTK 2.10)
if (is.null(gtkCheckVersion(2,10,0))) {
settings <- gtkSettingsGetDefault()
settings$set(gtk_enable_animations = F)
}
# create tooltips repository
.exp$setTooltips(gtkTooltips())
# create mainWindow window
mainWindow <- gtkWindow("toplevel", show = F)
.exp$setMainWindow(mainWindow)
mainWindow$setTitle(paste("exploRase", getExploraseVersion()))
mainWindow$setDefaultSize(950, 450)
mainWindow$setResizable(TRUE)
gSignalConnect(mainWindow, "delete-event", MnuExit_cb, quit_on_exit)
#### Create data models and views ####
# Entity Lists
.exp$setListModel(listModel())
.exp$setListView(listView(getListModel()))
listViewScroll <- scrollView(getListView())
# Entity Information
entityBook <- gtkNotebook()
.exp$setEntityBook(entityBook)
if (!(type %in% names(.exploraseTypes)))
exp_addEntityType(type)
sapply(names(.exploraseTypes), function(t) # register entity types
exp_addEntityType(t, .exploraseTypes[t]))
gSignalConnect(entityBook, "switch-page", entityBookSwitchPage_cb)
# Experimental Design
.exp$setDesignView(designView(getDesignModel(type)))
designViewScroll <- scrollView(getDesignView())
# Ready to set the entity type
setEntityType(type)
#### Define GUI actions ####
actionEntries <- list(
list("FileMenu", NULL, "_File"),
list("OpenFile", "gtk-open", "_Import File(s)", "<control>F",
"Select an individual file to load", MnuOpenFile_cb),
list("OpenProject", "gtk-goto-top", "_Open", "<control>O",
"Select an individual file to load", MnuOpenProject_cb),
list("SaveMenu", "gtk-save", "_Export"),
list("SaveEntityInfo", NULL, "Export Entity _Info", "<alt>I",
"Save entity information table", MnuSaveEntityInfo_cb),
list("SaveEntityLists", NULL, "Export Entity _Lists", "<alt>L",
"Save entity lists", MnuSaveEntityLists_cb),
list("SaveProject", "gtk-goto-bottom", "Save", "<control>R",
"Save entity information and entity lists", MnuSaveProject_cb),
list("Quit", "gtk-quit", "_Quit", "<control>Q", "Exit exploRase", MnuExit_cb),
#list("SaveDesignInfo", NULL, "_Design Info",
# "<alt>X", "Save experiment design information", MnuSaveDesignInfo_cb),
list("AnalysisMenu", NULL, "_Analysis"),
#list("CompareGenotypesMenu", NULL, "Compare _Genotypes"),
list("InterestingEntsMenu", NULL, "Find _Difference (two conditions)"),
list("SimilarEntsMenu", NULL, "Find _Similar (to selected entity)"),
list("ClusterMenu", NULL, "Find _Clusters"),
list("Patterns", NULL, "Find Specific _Pattern...", NULL,
"Open the pattern finding tool", MnuFindPattern_cb),
#list("Correlation", NULL, "Co_rrelation", NULL,
# "Find correlation between conditions", MnuCompareCorr_cb),
#list("Covariance", NULL, "Co_variance", NULL,
# "Find covariance between conditions", MnuCompareCov_cb),
list("Difference", NULL, "_Subtract", NULL,
"Subtract one condition from the other - good start", MnuDiff_cb),
list("Regression", NULL, "_Regression", NULL,
"Residuals from linear regression of conditions", MnuRegression_cb),
list("Angle", NULL, "_Angle", NULL,
"Angular distance from diagonal in scatterplot", MnuAngle_cb),
list("Mahalanobis", NULL, "_Mahalanobis", NULL,
"Distance from center of mass, assuming ellipse in scatterplot",
MnuMahalanobis_cb),
list("Euclidean", NULL, "_Euclidean", NULL,
"Compare by magnitude", MnuEuclidean_cb),
list("CorrelationDistance", NULL, "_Correlation", NULL,
"Compare by pattern", MnuCorr_cb),
list("ZeroCorr", NULL, "Cosine _Angle", NULL,
"Compare by pattern and magnitude", MnuZerocorr_cb),
list("Canberra", NULL, "Can_berra", NULL,
"Compare by normalized distance (good for zeros)", MnuCanberra_cb),
list("HClust", NULL, "_Hierarchical"),
list("HClustEuc", NULL, "_Euclidean", NULL, "Cluster by magnitude",
MnuHClust_euclidean_cb),
list("HClustCor", NULL, "_Correlation", NULL, "Cluster by pattern",
MnuHClust_cor_cb),
list("HClustAngle", NULL, "Cosine _Angle", NULL,
"Cluster by pattern and magnitude", MnuHClust_zerocor_cb),
list("HClustCan", NULL, "Can_berra", NULL,
"Cluster by Canberra distance (good for zeros)", MnuHClust_canberra_cb),
list("HClustSpearman", NULL, "_Spearman", NULL, "Cluster by rank pattern",
MnuHClust_spearman_cb),
list("DataMenu", NULL, "_Tools", NULL),
list("SubsetData", NULL, "_Subset/Filter...", NULL,
"Subset the experimental data based on various criteria", subset_cb),
list("AverageReplicates", NULL, "_Average over replicates", NULL,
"Create new variables for the means over the replicates", average_cb),
list("MedianReplicates", NULL, "_Median over replicates", NULL,
"Create new variables for the medians over the replicates", median_cb),
list("StdDevReplicates", NULL, "_Standard deviation over replicates", NULL,
"Create new variables for the standard deviations over the replicates", stddev_cb),
list("LogTransform", NULL, "_Log transform", NULL,
"Transform the data to the log scale", log_transform_cb),
list("ImportEntityInfoMenu", NULL, "Import Entity _Info"),
list("ClearColors", "gtk-clear", "_Clear Colors", NULL,
"Clear colors for selected genes (gray-out)", clearBtn_cb),
list("SyncColors", "gtk-refresh", "_Sync Colors", NULL,
"Synchronize colors with GGobi", updateBtn_cb),
list("CreateEntityList", "gtk-indent", "_Create List", NULL,
"Create a new entity list from selected rows in entity info table",
createList_cb),
list("QuerySources", "gtk-jump-to", "_ATGeneSearch", NULL,
"Access external data sources for information about selected entities",
browseBtn_cb),
list("ModelingMenu", NULL, "_Modeling"),
list("Limma", NULL, "_Linear modeling (limma)", NULL,
"Fit a linear model to the data using the Limma package",
limma_cb),
list("Temporal", NULL, "_Temporal modeling", NULL,
"Fit a polynomial time model",
temporal_cb),
list("GraphicsMenu", NULL, "_Graphics"),
list("Parcoords", NULL, "_Parallel coordinates plot", NULL,
"Create a parallel coordinates plot of the selected samples",
parcoords_cb),
list("Scatmat", NULL, "_Scatterplot matrix", NULL,
"Create a scatterplot matrix of the selected samples",
scatmat_cb),
list("MAplot", NULL, "_MAplot", NULL, "Create MAplot", MAplot_cb))
ag <- gtkActionGroup("exploRaseActions")
ag$addActions(actionEntries, mainWindow)
uiManager <- gtkUIManager()
.exp$setUIManager(uiManager)
uiManager$setAddTearoffs(T)
uiManager$insertActionGroup(ag, 0)
mainWindow$addAccelGroup(uiManager$getAccelGroup())
#### Create UI for actions ####
uiManager$addUiFromFile(system.file("ui", "ui.xml", package="explorase"))
menuBar <- uiManager$getWidget("/MenuBar")
toolBar <- uiManager$getWidget("/ToolBar")
# Add custom brush button to toolbar
colorBtn <- colorMenuToolButton(getGGobiColors())
toolBar$insert(colorBtn, 2)
# Remember the filled area for this button (to get brush color)
.exp$setBrushArea(colorBtn$getData("brush-area"))
# Link entity list selection to selection in entity info table
gSignalConnect(getListView()$getSelection(), "changed",
listSelectRow_cb)
# Design details button
designDetailsButton <- gtkButton("Details...")
gSignalConnect(designDetailsButton, "clicked", designDetailsButton_cb)
#### Statusbar ####
statusbar <- gtkHBox(F, 0)
progressBar <- gtkProgressBar()
statusbar$packStart(progressBar, T, T, 0)
taskBar <- gtkStatusbar()
taskBar$setSizeRequest(300, -1)
statusbar$packStart(taskBar, F, F, 0)
.exp$setStatusbar(statusbar)
#### Put everything together ####
glVbox <- gtkVBox(FALSE, 0)
designDetailsButtonBox <- gtkHBox()
designDetailsButtonBox$packStart(designDetailsButton, TRUE, FALSE, 0)
glVbox$packStart(designViewScroll, TRUE, TRUE, 0)
glVbox$packStart(designDetailsButtonBox, FALSE, FALSE, 2)
designFrame <- gtkFrame("Samples/Treatments")
designFrame$add(glVbox)
entityListFrame <- gtkFrame("Lists/Pathways")
entityListFrame$add(listViewScroll)
entityFrame <- gtkFrame("Entity Information")
entityFrame$add(entityBook)
vpan <- gtkVPaned()
hpan <- gtkHPaned()
vpan$pack1(designFrame, TRUE, TRUE)
vpan$pack2(entityListFrame, TRUE, TRUE)
hpan$pack1(vpan, TRUE, TRUE)
hpan$pack2(entityFrame, TRUE, TRUE)
hpan$setPosition(175)
mainWindowLayout <- gtkVBox(FALSE, 0)
mainWindowLayout$packStart(menuBar, FALSE, FALSE, 0)
mainWindowLayout$packStart(toolBar, FALSE, FALSE, 0)
mainWindowLayout$packStart(hpan, TRUE, TRUE, 0)
mainWindowLayout$packStart(statusbar, F, F, 0)
mainWindow$add(mainWindowLayout)
# work around gtk-fs-home icon 'bug'
# not known if this still exists in GTK 2.10
iconset <- mainWindow[["style"]]$lookupIconSet("gtk-home")
factory <- gtkIconFactoryNew()
factory$add("gnome-fs-home", iconset)
factory$addDefault()
#### Load any data passed at startup ####
if (!is.null(entity_info)) { # entity information
exp_loadInfo(entity_info, type)
}
if (!is.null(design_info)) { # experimental design information
exp_loadDesign(design_info, type)
}
if (is(exp_data, "ExpressionSet")) {
exp_loadExpressionSet(exp_data, type)
} else if (!is.null(exp_data)) { # experimental data
exp_loadData(exp_data, ent_type = type)
}
# networks would be loaded here...
if (!is.null(network))
exp_loadNetwork(network)
if (length(entity_lists) > 0) # entity lists
exp_loadLists(entity_lists)
#### Display GUI, finally ####
mainWindow$showAll()
# Final configuration of view columns
# This needs to be done at the end (after realization, I think)
configureViewColumns(getListView())
configureViewColumns(getDesignView())
sapply(getEntityViews(), configureViewColumns)
clearTask()
printOp("Welcome to exploRase: catalyze your analysis")
}
# Package info reflection
getExploraseVersion <- function() {
installed.packages()["explorase", "Version"]
}
# Check whether exploRase is running
# Currently a hack that checks if the main window exists
# @value whether exploRase is currently running
# @keyword GUI
exp_isRunning <- function() inherits(getMainWindow(), "GtkWindow")
exp_close <- function() {
getMainWindow()$destroy()
close(exp_ggobi())
}
# a project has been started, disable loading of more
projectStarted <- function() {
getAction("OpenProject")$setSensitive(FALSE)
}
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