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Merge branch 'develop' into scripts
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@LisaMc
LisaMc committed Mar 24, 2016
2 parents c48e219 + 77d07e6 commit 5e32ceb
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Showing 5 changed files with 1,003 additions and 194 deletions.
2 changes: 2 additions & 0 deletions Oncoscape/inst/scripts/blankTab/Module.js
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,7 @@ function sendSelections(event)
//--------------------------------------------------------------------------------------------
function handleSelections(msg)
{
hub.enableTab(thisModulesOutermostDiv);
hub.raiseTab(thisModulesOutermostDiv);
var msgAsString = JSON.stringify(msg.payload);

Expand Down Expand Up @@ -217,6 +218,7 @@ function initializeModule()
hub.addMessageHandler("sendSelectionTo_blankTab", handleSelections);
hub.addMessageHandler("blankTabAssessUserIdForTesting", assessUserIdForTesting)
hub.addSocketConnectedFunction(runAutomatedTestsIfAppropriate);
hub.enableTab(thisModulesOutermostDiv);

} // initializeModule
//----------------------------------------------------------------------------------------------------
Expand Down
170 changes: 74 additions & 96 deletions Oncoscape/inst/scripts/markersAndSamples/Module.js
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Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
//----------------------------------------------------------------------------------------------------
// move these all back inside module scope when debugging is done

// declare the cytoscape object in global scope, permitting easy manipulation in the javascript console.
var cwMarkers;
var markersTester;

//----------------------------------------------------------------------------------------------------
var markersAndTissuesModule = (function () {
Expand Down Expand Up @@ -76,10 +74,6 @@ function initializeUI ()
markersShowEdgesFromButton.click(showEdgesFromSelectedNodes);
hub.disableButton(markersShowEdgesFromButton);

//$("#markersFitViewButton").click(function(){cwMarkers.fit();});
//$("#markersHideEdgesButton").click(hideAllEdges);
//$("#markersShowEdgesFromSelectedButton").click(showEdgesFromSelectedNodes);

tumorCategorizationsMenu = $("#cyMarkersTumorCategorizationsMenu");
tumorCategorizationsMenu.empty();
tumorCategorizationsMenu.append("<option>" + tumorCategorizationsMenuTitle + "</option>");
Expand Down Expand Up @@ -207,17 +201,22 @@ function sendSelections(event)

} // sendSelections
//--------------------------------------------------------------------------------------------
function configureLayoutsMenu(layoutMenu){

// we currently support a limited amount cyjs layout save and restore.
// among the limitations are:
// a) they are saved on the user's computer
// b) they can only be retrieved if the same computer, the same browser, and the same url
// is used
function configureLayoutsMenu(layoutMenu)
{
console.log("--- configureLayoutsMenu");
layoutMenu.append("<option>Layouts...</option>");
layoutMenu.append("<option> Save Current</option>");

var defaultLayout = JSON.stringify(cwMarkers.nodes().map(function(n){
var result = {id:n.id(), position:n.position()};
return (result);
}) // map
); // stringify
var result = {id:n.id(), position:n.position()};
return (result);
}) // map
); // stringify

localStorage.markersDefault = defaultLayout;

Expand Down Expand Up @@ -260,20 +259,6 @@ function performLayout(event){

} // performLayout
//--------------------------------------------------------------------------------------------
function sendSelection()
{
destinationModule = sendSelectionsMenu.val();
var nodeNames = selectedNodeNames(cwMarkers);
if(nodeNames.length === 0){
console.log("no nodes selected!");
return;
}
metadata = {};
sendSelectionToModule(destinationModule, nodeNames, metadata);
sendSelectionsMenu.val("Send Selection...");

} // sendSelectionsMenuChanged
//--------------------------------------------------------------------------------------------
function configureCytoscape ()
{
cwMarkers = $("#cyMarkersDiv");
Expand Down Expand Up @@ -330,12 +315,13 @@ function configureCytoscape ()

} // configureCytoscape
//----------------------------------------------------------------------------------------------------
function handleWindowResize ()
function handleWindowResize()
{
cyDiv.width(0.95 * $(window).width());
cyDiv.height(0.8 * $(window).height());
// todo: should preserve preceeding view.
cwMarkers.resize();
cwMarkers.fit(50);
cwMarkers.fit(50);

} // handleWindowResize
//----------------------------------------------------------------------------------------------------
Expand All @@ -362,12 +348,17 @@ function debounce(func, wait, immediate)
// expand node size and display node labels when:
// 1) the user's coordinate space, due to zooming, has shrunk to < 600 pixels
// 2) the zoom factor is so large relative to the initial zoom (a global variable, set on startup)
//
//
// the current implemetation is decidely imperfect. the operations accomplished here take too
// long, creating a sometimes quite unsatisfying user experience.
// this has been mitigated somewhat by
// - deboucncing (at some interval)
// - expanding nodes, adjusting font, node border and edge width only when well zoomed in
// AND a modest number of nodes are onscreen
// - trying to avoid layout when possible in the base network.
//
function smartZoom(event)
{
//console.log("smartZoom");
var queuedEvents = $("#cyMarkersDiv").queue();

var zoomRatio = cwMarkers.zoom()/initialZoom;
console.log("zoomRatio: " + zoomRatio);

Expand All @@ -380,8 +371,6 @@ function smartZoom(event)
var visibleOnScreen = function(node){
if(node.data("landmark"))
return(false);
//var x = node.position().x;
//var y = node.position().y;
var bbox = node.boundingBox();
var visibleX = (bbox.x1 >= visibleCoords.x1 && bbox.x1 <= visibleCoords.x2) |
(bbox.x2 >= visibleCoords.x1 && bbox.x2 <= visibleCoords.x2);
Expand All @@ -390,27 +379,17 @@ function smartZoom(event)
var visibleY = (bbox.y1 >= visibleCoords.y1 && bbox.y1 <= visibleCoords.y2) |
(bbox.y2 >= visibleCoords.y1 && bbox.y2 <= visibleCoords.y2);
return(visibleY);
//return(x >= visibleCoords.x1 && x <= visibleCoords.x2 &&
// y >= visibleCoords.y1 && y <= visibleCoords.y2);
};

//console.log("starting calculation of visibleNodes");
var visibleNodes = cwMarkers.nodes().fnFilter(function(node){return(visibleOnScreen(node));});
console.log("visibleNode count: " + visibleNodes.length);
if(visibleNodes.length > 400){
defaultStyle();
//console.log("returning, visibleNode count: " + visibleNodes.length);
return;
}
//console.log("need to smartZoom, setting hanlder off to discard queued events");
//cwMarkers.off('zoom', smartZoom);

//console.log(event);
var newZoom = 1.0 + cwMarkers.zoom() - oldZoom;
oldZoom = cwMarkers.zoom(); // keep this for next time

//console.log("complete");

// TODO: these two ratios might be reduced to just one

var windowRatio = cwMarkers.width()/cwMarkers.extent().h;
Expand All @@ -421,8 +400,6 @@ function smartZoom(event)

var fontSizeString = fontSize + "px";
var borderWidthString = cwMarkers.extent().h/600 + "px";
//console.log("--- new fontsize: " + fontSizeString);
//console.log("--- new borderWidth: " + borderWidthString);
cwMarkers.edges().style({"width": borderWidthString});

var newWidth, newHeight, id;
Expand All @@ -438,23 +415,21 @@ function smartZoom(event)
});
});

//console.log("visibleNode mapping complete, adding smartZoom handler back");
//cwMarkers.on('zoom', smartZoom);


} // smartZoom
//----------------------------------------------------------------------------------------------------
// undo any changes brought about during smartZoom.
// TODO: it seems a better approach would be to remove the zoomed attribute, and apply the style rules
// everywhere with which the network was initialized.
function defaultStyle()
{
var zoomedNodes = cwMarkers.nodes("[zoomed]");
// console.log("restoring default style, zoomed node count: " + zoomedNodes.length);
cwMarkers.edges().style({"width": "1px"});

zoomedNodes.map(function(node){node.style({width: node.data('trueWidth'),
height: node.data('trueHeight'),
zoomedNodes.map(function(node){node.style({width: node.data("trueWidth"),
height: node.data("trueHeight"),
zoomed: false,
'border-width': "1px",
'font-size': "3px"});});
"border-width": "1px",
"font-size": "3px"});});

} // defaultStyle
//----------------------------------------------------------------------------------------------------
Expand All @@ -466,8 +441,11 @@ function defaultStyle()
//
function subSelectNodes()
{
// var selectedPatientNodes = cwMarkers.nodes("node[nodeType='patient']:selected"); comment necessary to handle quotation issue
var selectedPatientNodes = cwMarkers.nodes("node[nodeType='patient']:selected");
var categories = jQuery.unique(selectedPatientNodes.map(function(e){return e.data("category");}));
var categories = jQuery.unique(
selectedPatientNodes.map(function(e){
return e.data("category");}));

var colors = jQuery.unique(selectedPatientNodes.map(function(node){return (node.style("background-color"));}));

Expand Down Expand Up @@ -550,25 +528,52 @@ function requestTumorCategorization()

} // requestTumorCategorization
//----------------------------------------------------------------------------------------------------
// msg.payload has 3 fields: colnames, rownames, tbl
// colnames: ["cluster", "color"]
// rownames: possibly large number of tumors (samples) with category (cluster) & color assigned
// tbl: a matrix, rownames.length x colnames.lenght, of cluster and color assignments
// representing this data structure
// cluster color
// TCGA.08.0525 Classical chocolate
// ...
//
// strategy:
// get unique cluster/color pairs (far fewer of these, typically, than sample ids (tbl rows).
// each sample named in the tbl, and also found in the network, will get a "category" (aka "cluster")
// attribute assigned to it near the end of this function.
// first, however, cyjs/css style rules are handcrafted, one for unique cluster value, and one
// for each cluster value if the node is selected.

function applyTumorCategorization(msg)
{
console.log("=== applyTumorCategorization");

var tumorsInGraph = cwMarkers.nodes("[nodeType='patient']");
var tumorsInTable = msg.payload.rownames;
var tbl = msg.payload.tbl;
var categoryRules = {};
tbl.forEach(function(row){categoryRules[row[0]] = row[1];});

// this forEach loop inelegantly reduces many rows to a unique set
// by overwriting, e.g., categoryRules["G-CIMP"] = "purple" each of
// the time it is seen. this inefficiency could be eliminated by
// sending across just the unique rules from R as a payload field
// (and also removing the color column from tbl).

tbl.forEach(function(row){categoryRules[row[0]] = row[1];});

/* jshint ignore:start */
//debugger;
/* jshint ignore:end */

categoryRuleNames = Object.keys(categoryRules);
// e.g. ["G-CIMP", "Classical", "null", "Proneural", "Neural", "Mesenchymal"]
categoryRuleNames.filter(function(name){return name !== "null";});
categoryRuleNames.filter(function(name){return name !== null;});
var newRules = [];

// translate the categoryRules into cyjs/css style rules, which
// look like this:
// {"selector":"node[category='Classical']","style":{"background-color":"chocolate"}}
// {"selector":"node[category='Classical']:selected",
// "style":{"border-color":"red","background-color":"chocolate","border-width":"10px"}}"

categoryRuleNames.forEach(function(name){
var selector = "node[category='" + name + "']";
color=categoryRules[name];
Expand All @@ -592,6 +597,10 @@ function applyTumorCategorization(msg)

hub.logEventOnServer(thisModulesName, "markersApplyTumorCategorization", "data received", "");

// iterate across the tumor ('patient') nodes, add a category attribute, assign
// a cluster value from the tbl, which will select one of the style rules just
// created above.

console.log("starting tumorsInGraph.forEach");
cwMarkers.batch(function() {
tumorsInGraph.forEach(function(node, index){
Expand All @@ -610,6 +619,9 @@ function applyTumorCategorization(msg)

console.log("ending tumorsInGraph.forEach");

// get a copy of the current style, remove any old node-category style rules, add the new ones
// set this new style

var oldStyle = cwMarkers.style().json();
// remove any pre-existing node category rules
var oldStyleClean = oldStyle.filter(function(e){return(e.selector.indexOf("node[category"));});
Expand Down Expand Up @@ -747,40 +759,6 @@ function handleIncomingIdentifiers(msg)
hub.raiseTab(thisModulesOutermostDiv);

} // handleIncomingIdentifiers
//----------------------------------------------------------------------------------------------------
// run all that should happen when this module receives an incoming selection of patientIDs
function demoMarkersIncomingSelectionOfIDs()
{

names = ["TCGA.06.0210", "TCGA.02.0106", "TCGA.02.0111",
"TCGA.06.0194", "TCGA.06.0164", "TCGA.06.0409", "TCGA.02.0004",
"TCGA.02.0051", "TCGA.08.0390", "TCGA.02.0025", "TCGA.08.0392",
"TCGA.02.0079", "TCGA.12.0620", "TCGA.08.0373", "TCGA.06.0645",
"TCGA.06.0192", "TCGA.12.0776", "TCGA.12.0778", "TCGA.06.0750",
"TCGA.06.0878", "TCGA.14.0789", "TCGA.06.0881", "BCL11A",
"BRCA1", "MDM2", "PIK3R1", "ABCA1", "CDK6", "CNTRL", "FH",
"IFNA1", "LMO2", "PRKCA", "RELA", "STK11", "ZEB1", "CCNB1IP1",
"CREB3L1", "GDF2", "OR4K2", "PRKCH", "WAS"];

subset = [];
for(var i=0; i < 10; i++)
subset.push(names[getRandomInt(0, names.length -1)]);

selectNodes(subset);

} // demoIncomingSelectionOfPatientIDs
//----------------------------------------------------------------------------------------------------
function allNodeIDs()
{
ids = [];
allNodes = cwMarkers.nodes();

for(i=0; i < allNodes.length; i++)
ids.push(allNodes[i].data("id"));

return(ids);

} // allNodeIDs
//----------------------------------------------------------------------------------------------------
function showEdges()
{
Expand Down Expand Up @@ -1028,7 +1006,7 @@ function selectNodes(nodeNames)

} // selectNodes
//----------------------------------------------------------------------------------------------------
// todo: build up the filter string first, then send it all at once
// todo: build up the filter string first, then send it all at once
function selectNodesByID(nodeIDs) {

if(typeof(nodeIDs) == "string") // trap scalar, but expect and support arrays
Expand Down
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