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morpheus.js
Commit e599771c authored by Daria Zenkova's avatar Daria Zenkova
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fixing support of colour and size as options for ggplot

parent 13d4dca9
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Showing with 978 additions and 50 deletions
Gruntfile.js
View file @ e599771c
......@@ -67,7 +67,8 @@ module.exports = function (grunt) {
'js/jquery.event.drag-2.2.js',
'js/clipboard.min.js', 'js/slick.min.js',
'js/js.cookie.js', 'js/d3.layout.cloud.js',
'js/long.js', 'js/bytebuffer.js', 'js/protobuf.js']
'js/long.js', 'js/bytebuffer.js', 'js/protobuf.js',
'js/opencpu-0.5.js', 'js/FileSaver.min.js']
},
morpheus: {
nonull: true,
......
index.html
View file @ e599771c
......@@ -10,6 +10,10 @@
<title>Morpheus</title>
<link rel="stylesheet" href="css/morpheus-latest.min.css">
<script type="text/javascript" src="js/morpheus-external-latest.min.js"></script>
<script>
ocpu.seturl("http://localhost:7963/ocpu/library/morpheusR/R");
</script>
<script src="js/morpheus-latest.min.js"></script>
<script src="js/jsme/jsme.nocache.js"></script>
<link href="https://fonts.googleapis.com/css?family=Roboto"
......
js/FileSaver.min.js
View file @ e599771c
/*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/FileSaver.js */
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\ No newline at end of file
js/morpheus-external-latest.min.js
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js/morpheus-latest.min.js
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js/opencpu-0.5.js 0 → 100644
View file @ e599771c
/**
* Javascript client library for OpenCPU
* Version 0.5.0
* Depends: jQuery
* Requires HTML5 FormData support for file uploads
* http://github.com/jeroenooms/opencpu.js
*
* Include this file in your apps and packages.
* You only need to use ocpu.seturl if this page is hosted outside of the OpenCPU package. For example:
*
* ocpu.seturl("../R") //default, use for apps
* ocpu.seturl("//public.opencpu.org/ocpu/library/mypackage/R") //CORS
* ocpu.seturl("/ocpu/library/mypackage/R") //hardcode path
* ocpu.seturl("https://user:secret/my.server.com/ocpu/library/pkg/R") // basic auth
*/
//Warning for the newbies
if(!window.jQuery) {
alert("Could not find jQuery! The HTML must include jquery.js before opencpu.js!")
}
(function ( $ ) {
//global variable
var r_cors = false;
var r_path = document.createElement('a');
r_path.href = "../R";
//new Session()
function Session(loc, key, txt){
this.loc = loc;
this.key = key;
this.txt = txt;
this.output = txt.split(/\r\n|\r|\n/g);
this.getKey = function(){
return key;
};
this.getLoc = function(){
return loc;
};
this.getFileURL = function(path){
var new_url = document.createElement('a');
new_url.href = this.getLoc() + "files/" + path;
new_url.username = r_path.username;
new_url.password = r_path.password
return new_url.href;
};
this.getFile = function(path, success){
var url = this.getFileURL(path);
return $.get(url, success);
};
this.getObject = function(name, data, success){
//in case of no arguments
name = name || ".val";
//first arg is a function
if(name instanceof Function){
//pass on to second arg
success = name;
name = ".val";
}
var url = this.getLoc() + "R/" + name;
return $.get(url, data, success);
};
this.getGraphics = function (index, data, success) {
index = index || 1;
var url = this.getLoc() + "graphics/" + index;
return $.get(url, data, success);
};
this.getStdout = function(success){
var url = this.getLoc() + "stdout/text";
return $.get(url, success);
};
this.getConsole = function(success){
var url = this.getLoc() + "console/text";
return $.get(url, success);
};
}
//for POSTing raw code snippets
//new Snippet("rnorm(100)")
function Snippet(code){
this.code = code || "NULL";
this.getCode = function(){
return code;
};
}
//for POSTing files
//new Upload($('#file')[0].files)
function Upload(file){
if(file instanceof File){
this.file = file;
} else if(file instanceof FileList){
this.file = file[0];
} else if (file.files instanceof FileList){
this.file = file.files[0];
} else if (file.length > 0 && file[0].files instanceof FileList){
this.file = file[0].files[0];
} else {
throw 'invalid new Upload(file). Argument file must be a HTML <input type="file"></input>';
}
this.getFile = function(){
return file;
};
}
function stringify(x){
if(x instanceof Session){
return x.getKey();
} else if(x instanceof Snippet){
return x.getCode();
} else if(x instanceof Upload){
return x.getFile();
} else if(x instanceof File){
return x;
} else if(x instanceof FileList){
return x[0];
} else if(x && x.files instanceof FileList){
return x.files[0];
} else if(x && x.length && x[0].files instanceof FileList){
return x[0].files[0];
} else {
return JSON.stringify(x);
}
}
//low level call
function r_fun_ajax(fun, settings, handler){
//validate input
if(!fun) throw "r_fun_call called without fun";
settings = settings || {};
handler = handler || function(){};
//set global settings
settings.url = settings.url || (r_path.href + "/" + fun);
settings.type = settings.type || "POST";
settings.data = settings.data || {};
settings.dataType = settings.dataType || "text";
//ajax call
var jqxhr = $.ajax(settings).done(function(){
var loc = jqxhr.getResponseHeader('Location') || console.log("Location response header missing.");
var key = jqxhr.getResponseHeader('X-ocpu-session') || console.log("X-ocpu-session response header missing.");
var txt = jqxhr.responseText;
//in case of cors we translate relative paths to the target domain
if(r_cors && loc.match("^/[^/]")){
loc = r_path.protocol + "//" + r_path.host + loc;
}
handler(new Session(loc, key, txt));
}).fail(function(){
console.log("OpenCPU error HTTP " + jqxhr.status + "\n" + jqxhr.responseText);
});
//function chaining
return jqxhr;
}
//call a function using protobuf arguments
function r_fun_call_proto(fun, args, handler) {
return r_fun_ajax(fun, {
data : new Uint8Array(args.toArrayBuffer()),
contentType : 'application/x-protobuf',
processData : false
}, handler);
}
//call a function using json arguments
function r_fun_call_json(fun, args, handler) {
return r_fun_ajax(fun, {
data: JSON.stringify(args || {}),
contentType: 'application/json'
}, handler);
}
//call function using url encoding
//needs to wrap arguments in quotes, etc
function r_fun_call_urlencoded(fun, args, handler){
var data = {};
$.each(args, function(key, val){
data[key] = stringify(val);
});
return r_fun_ajax(fun, {
data: $.param(data)
}, handler);
}
//call a function using multipart/form-data
//use for file uploads. Requires HTML5
function r_fun_call_multipart(fun, args, handler){
testhtml5();
var formdata = new FormData();
$.each(args, function(key, value) {
formdata.append(key, stringify(value));
});
return r_fun_ajax(fun, {
data: formdata,
cache: false,
contentType: false,
processData: false
}, handler);
}
//Automatically determines type based on argument classes.
function r_fun_call(fun, args, handler, useProtobuf){
useProtobuf = useProtobuf || false;
args = args || {};
var hasfiles = false;
var hascode = false;
//find argument types
$.each(args, function(key, value){
if(value instanceof File || value instanceof Upload || value instanceof FileList){
hasfiles = true;
} else if (value instanceof Snippet || value instanceof Session){
hascode = true;
}
});
//determine type
if(hasfiles){
return r_fun_call_multipart(fun, args, handler);
} else if(hascode){
return r_fun_call_urlencoded(fun, args, handler);
} else if (useProtobuf) {
return r_fun_call_proto(fun, args, handler);
} else {
return r_fun_call_json(fun, args, handler);
}
}
//call a function and return JSON
function rpc(fun, args, handler, useProtobuf){
useProtobuf = useProtobuf || false;
return r_fun_call(fun, args, function(session){
session.getObject(function(data){
if(handler) handler(data);
}).fail(function(){
console.log("Failed to get JSON response for " + session.getLoc());
});
}, useProtobuf);
}
//plotting widget
//to be called on an (empty) div.
$.fn.rplot = function(fun, args, cb) {
var targetdiv = this;
var myplot = initplot(targetdiv);
//reset state
myplot.setlocation();
myplot.spinner.show();
// call the function
return r_fun_call(fun, args, function(tmp) {
myplot.setlocation(tmp.getLoc());
//call success handler as well
if(cb) cb(tmp);
}).always(function(){
myplot.spinner.hide();
});
};
$.fn.graphic = function(session, n){
initplot(this).setlocation(session.getLoc(), n || "last");
}
function initplot(targetdiv){
if(targetdiv.data("ocpuplot")){
return targetdiv.data("ocpuplot");
}
var ocpuplot = function(){
//local variables
var Location;
var n = "last";
var pngwidth;
var pngheight;
var plotdiv = $('<div />').attr({
style: "width: 100%; height:100%; min-width: 100px; min-height: 100px; position:relative; background-repeat:no-repeat; background-size: 100% 100%;"
}).appendTo(targetdiv).css("background-image", "none");
var spinner = $('<span />').attr({
style : "position: absolute; top: 20px; left: 20px; z-index:1000; font-family: monospace;"
}).text("loading...").appendTo(plotdiv).hide();
var pdf = $('<a />').attr({
target: "_blank",
style: "position: absolute; top: 10px; right: 10px; z-index:1000; text-decoration:underline; font-family: monospace;"
}).text("pdf").appendTo(plotdiv);
var svg = $('<a />').attr({
target: "_blank",
style: "position: absolute; top: 30px; right: 10px; z-index:1000; text-decoration:underline; font-family: monospace;"
}).text("svg").appendTo(plotdiv);
var png = $('<a />').attr({
target: "_blank",
style: "position: absolute; top: 50px; right: 10px; z-index:1000; text-decoration:underline; font-family: monospace;"
}).text("png").appendTo(plotdiv);
function updatepng(){
if(!Location) return;
pngwidth = plotdiv.width();
pngheight = plotdiv.height();
plotdiv.css("background-image", "url(" + Location + "graphics/" + n + "/png?width=" + pngwidth + "&height=" + pngheight + ")");
}
function setlocation(newloc, newn){
n = newn || n;
Location = newloc;
if(!Location){
pdf.hide();
svg.hide();
png.hide();
plotdiv.css("background-image", "");
} else {
pdf.attr("href", Location + "graphics/" + n + "/pdf?width=11.69&height=8.27&paper=a4r").show();
svg.attr("href", Location + "graphics/" + n + "/svg?width=11&height=6").show();
png.attr("href", Location + "graphics/" + n + "/png?width=800&height=600").show();
updatepng();
}
}
// function to update the png image
var onresize = debounce(function(e) {
if(pngwidth == plotdiv.width() && pngheight == plotdiv.height()){
return;
}
if(plotdiv.is(":visible")){
updatepng();
}
}, 500);
// register update handlers
plotdiv.on("resize", onresize);
$(window).on("resize", onresize);
//return objects
return {
setlocation: setlocation,
spinner : spinner
};
}();
targetdiv.data("ocpuplot", ocpuplot);
return ocpuplot;
}
// from understore.js
function debounce(func, wait, immediate) {
var result;
var timeout = null;
return function() {
var context = this, args = arguments;
var later = function() {
timeout = null;
if (!immediate)
result = func.apply(context, args);
};
var callNow = immediate && !timeout;
clearTimeout(timeout);
timeout = setTimeout(later, wait);
if (callNow)
result = func.apply(context, args);
return result;
};
}
function testhtml5(){
if( window.FormData === undefined ) {
alert("Uploading of files requires HTML5. It looks like you are using an outdated browser that does not support this. Please install Firefox, Chrome or Internet Explorer 10+");
throw "HTML5 required.";
}
}
//export
window.ocpu = window.ocpu || {};
var ocpu = window.ocpu;
//global settings
function seturl(newpath){
if(!newpath.match("/R$")){
alert("ERROR! Trying to set R url to: " + newpath +". Path to an OpenCPU R package must end with '/R'");
} else {
r_path = document.createElement('a');
r_path.href = newpath;
r_path.href = r_path.href; //IE needs this
if(location.protocol != r_path.protocol || location.host != r_path.host){
r_cors = true;
if (!('withCredentials' in new XMLHttpRequest())) {
alert("This browser does not support CORS. Try using Firefox or Chrome.");
} else if(r_path.username && r_path.password) {
//should only do this for calls to opencpu maybe
var regex = new RegExp(r_path.host);
$.ajaxSetup({
beforeSend: function(xhr, settings) {
//only use auth for ajax requests to ocpu
if(regex.test(settings.url)){
//settings.username = r_path.username;
//settings.password = r_path.password;
/* take out user:pass from target url */
var target = document.createElement('a');
target.href = settings.url;
settings.url = target.protocol + "//" + target.host + target.pathname
/* set basic auth header */
settings.xhrFields = settings.xhrFields || {};
settings.xhrFields.withCredentials = true;
settings.crossDomain = true;
xhr.setRequestHeader("Authorization", "Basic " + btoa(r_path.username + ":" + r_path.password));
/* debug */
console.log("Authenticated request to: " + settings.url + " (" + r_path.username + ", " + r_path.password + ")")
}
}
});
}
}
if(location.protocol == "https:" && r_path.protocol != "https:"){
alert("Page is hosted on HTTPS but using a (non-SSL) HTTP OpenCPU server. This is insecure and most browsers will not allow this.")
}
if(r_cors){
console.log("Setting path to CORS server " + r_path.href);
} else {
console.log("Setting path to local (non-CORS) server " + r_path.href);
}
//CORS disallows redirects.
return $.get(r_path.href + "/", function(resdata){
//console.log("Path updated. Available objects/functions:\n" + resdata);
}).fail(function(xhr, textStatus, errorThrown){
alert("Connection to OpenCPU failed:\n" + textStatus + "\n" + xhr.responseText + "\n" + errorThrown);
});
}
}
//exported functions
ocpu.call = r_fun_call;
ocpu.rpc = rpc;
ocpu.seturl = seturl;
ocpu.mycall = r_fun_ajax;
//exported constructors
ocpu.Snippet = Snippet;
ocpu.Upload = Upload;
//for innernetz exploder
if (typeof console == "undefined") {
this.console = {log: function() {}};
}
}( jQuery ));
src/io/tcga_util.js
View file @ e599771c
......@@ -334,6 +334,7 @@ morpheus.TcgaUtil.getDataset = function (options) {
f(datasetToReturn);
});
}
datasetToReturn.setESSession();
returnDeferred.resolve(datasetToReturn);
});
return returnDeferred;
......
src/matrix/dataset.js
View file @ e599771c
......@@ -160,6 +160,33 @@ morpheus.Dataset.prototype = {
this.seriesArrays.push(options.array != null ? options.array
: morpheus.Dataset.createArray(options));
return this.seriesNames.length - 1;
},
setESSession : function () {
var _this = this;
if (this.esSession != null) {
return this.esSession;
}
else {
var protoMessage = morpheus.DatasetUtil.toProtoMessage(this);
var blob = new Blob(new Uint8Array(protoMessage), {type: "application/octet-stream"});
saveAs(blob, "test.bin");
var req = ocpu.call("createES", protoMessage, function (session) {
console.log(session);
_this.esSession = session;
}, true);
req.fail(function () {
alert("failed to create ExpressionSet of dataset");
})
}
},
getESSession : function () {
if (this.esSession == null) {
this.setESSession();
}
return this.esSession;
}
};
morpheus.Util.extend(morpheus.Dataset, morpheus.AbstractDataset);
\ No newline at end of file
src/matrix/dataset_util.js
View file @ e599771c
......@@ -805,3 +805,118 @@ morpheus.DatasetUtil.getNonEmptyRows = function (dataset) {
}
return rowsToKeep;
};
morpheus.DatasetUtil.getContentArray = function (dataset) {
var array = [];
var nr = dataset.rows;
var nc = dataset.columns;
for (var i = 0; i < nr; i++) {
for (var j = 0; j < nc; j++) {
array.push(dataset.getValue(i, j));
}
}
return array;
};
morpheus.DatasetUtil.getMetadataArray = function (dataset) {
var pDataArray = [];
var participantID = [];
var labelDescription = [];
var columnMeta = dataset.getColumnMetadata();
var n = columnMeta.getMetadataCount();
var m = dataset.columns;
for (var i = 0; i < n; i++) {
var vecI = columnMeta.get(i);
if (vecI.getName() == "participant_id") {
for (var j = 0; j < m; j++) {
participantID.push({
strval : vecI.getValue(j),
isNA : false
});
}
}
else {
for (j = 0; j < m; j++) {
pDataArray.push({
strval : vecI.getValue(j).toString(),
isNA : false
});
}
labelDescription.push({
strval : vecI.getName(),
isNA : false
});
}
}
var rowMeta = dataset.getRowMetadata();
var rowNames = [];
var rowNamesVec = rowMeta.getByName("id");
for (j = 0; j < dataset.rows; j++) {
rowNames.push({
strval : rowNamesVec.getValue(j),
isNA : false
})
}
return {pdata : pDataArray, participants : participantID, labels : labelDescription, rownames : rowNames};
};
morpheus.DatasetUtil.toProtoMessage = function (dataset) {
var array = morpheus.DatasetUtil.getContentArray(dataset);
var meta = morpheus.DatasetUtil.getMetadataArray(dataset);
var messageJSON = {
rclass : "LIST",
rexpValue : [{
rclass : "REAL",
realValue : array,
attrName : "dim",
attrValue : {
rclass : "INTEGER",
intValue : [dataset.rows, dataset.columns]
}
}, {
rclass : "STRING",
stringValue : meta.pdata,
attrName : "dim",
attrValue : {
rclass : "INTEGER",
intValue : [dataset.getColumnMetadata().getMetadataCount() - 1, dataset.columns]
}
}, {
rclass : "STRING",
stringValue : meta.labels
}, {
rclass : "STRING",
stringValue : meta.participants
}, {
rclass : "STRING",
stringValue : meta.rownames
}],
attrName : "names",
attrValue : {
rclass : "STRING",
stringValue : [{
strval : "data",
isNA : false
}, {
strval : "pData",
isNA : false
}, {
strval : "labelDescription",
isNA : false
}, {
strval : "colNames",
isNA : false
}, {
strval : "rowNames",
isNA : false
}]
}
};
ProtoBuf = dcodeIO.ProtoBuf;
var builder = ProtoBuf.protoFromFile("./message.proto"),
rexp = builder.build("rexp"),
REXP = rexp.REXP;
return new REXP(messageJSON);
};
\ No newline at end of file
src/matrix/project.js
View file @ e599771c
......@@ -13,6 +13,7 @@ morpheus.Project = function(dataset) {
this.columnSelectionModel = new morpheus.SelectionModel(this, true);
this.rowSelectionModel = new morpheus.SelectionModel(this, false);
this.elementSelectionModel = new morpheus.ElementSelectionModel(this);
morpheus.Project._recomputeCalculatedFields(this.originalDataset);
morpheus.Project
._recomputeCalculatedFields(new morpheus.TransposedDatasetView(
......@@ -99,6 +100,8 @@ morpheus.Project.prototype = {
this.columnSelectionModel.clear();
this.rowSelectionModel.clear();
this.elementSelectionModel.clear();
this.setESSession(dataset);
if (notify) {
this.trigger(morpheus.Project.Events.DATASET_CHANGED);
}
......
src/tools/pcaplot_tool.js
View file @ e599771c
morpheus.PcaPlotTool = function (chartOptions) {
var _this = this;
this.getVisibleTrackNames = chartOptions.getVisibleTrackNames;
this.project = chartOptions.project;
var project = this.project;
var nr = project.getRowSelectionModel().count();
if (nr != 2) {
alert("Choose exactly two rows to construct pcaPlot");
}
var nc = project.getColumnSelectionModel().count();
if (nc == 0) {
alert("Choose some columns");
}
var selectedDataset = project.getSelectedDataset();
this.$el = $('<div class="container-fluid">'
+ '<div class="row">'
+ '<div data-name="configPane" class="col-xs-2"></div>'
+ '<div class="col-xs-10"><div style="position:relative;" data-name="chartDiv"></div></div>'
+ '</div></div>');
console.log(selectedDataset);
console.log(nr, nc);
var formBuilder = new morpheus.FormBuilder({
vertical: true
});
this.formBuilder = formBuilder;
var rowOptions = [];
var columnOptions = [];
var numericRowOptions = [];
var numericColumnOptions = [];
var options = [];
var numericOptions = [];
var updateOptions = function () {
var dataset = project.getFullDataset();
rowOptions = [{
name: '(None)',
value: ''
}];
columnOptions = [{
name: '(None)',
value: ''
}];
numericRowOptions = [{
name: '(None)',
value: ''
}];
numericColumnOptions = [{
name: '(None)',
value: ''
}];
options = [{
name: '(None)',
value: ''
}];
numericOptions = [{
name: '(None)',
value: ''
}];
morpheus.MetadataUtil.getMetadataNames(dataset.getRowMetadata())
.forEach(
function (name) {
var dataType = morpheus.VectorUtil
.getDataType(dataset.getRowMetadata()
.getByName(name));
if (dataType === 'number'
|| dataType === '[number]') {
numericRowOptions.push({
name: name + ' (row)',
value: name
});
}
rowOptions.push({
name: name + ' (row)',
value: name
});
});
morpheus.MetadataUtil.getMetadataNames(dataset.getColumnMetadata())
.forEach(
function (name) {
var dataType = morpheus.VectorUtil
.getDataType(dataset.getColumnMetadata()
.getByName(name));
if (dataType === 'number'
|| dataType === '[number]') {
numericColumnOptions.push({
name: name + ' (column)',
value: name
});
}
columnOptions.push({
name: name + ' (column)',
value: name
});
});
options = options.concat(rowOptions.slice(1));
options = options.concat(columnOptions.slice(1));
numericOptions = numericOptions.concat(numericRowOptions.slice(1));
numericOptions = numericOptions.concat(numericColumnOptions.slice(1));
};
updateOptions();
formBuilder.append({
name: 'group_columns_by',
type: 'bootstrap-select',
options: options
});
formBuilder.append({
name: 'group_rows_by',
type: 'bootstrap-select',
options: options
});
formBuilder.append({
name: 'size',
type: 'bootstrap-select',
options: numericOptions
});
formBuilder.append({
name: 'color',
type: 'bootstrap-select',
options: numericOptions
});
function setVisibility() {
formBuilder.setOptions('color', options, true);
formBuilder.setOptions('size', numericOptions, true);
}
this.tooltip = [];
formBuilder.$form.find('select').on('change', function (e) {
if ($(this).attr('name') === 'tooltip') {
var tooltipVal = _this.formBuilder.getValue('tooltip');
_this.tooltip = [];
if (tooltipVal != null) {
tooltipVal.forEach(function (tip) {
_this.tooltip.push(morpheus.ChartTool.getVectorInfo(tip));
});
}
} else {
setVisibility();
_this.draw();
}
});
formBuilder.$form.find('input').on('click', function () {
_this.draw();
});
setVisibility();
var draw = function () {
_.debounce(_this.draw(), 100);
};
var trackChanged = function () {
updateOptions();
setVisibility();
formBuilder.setOptions('group_columns_by', options, true);
formBuilder.setOptions('group_rows_by', options, true);
};
project.getColumnSelectionModel().on('selectionChanged.chart', draw);
project.getRowSelectionModel().on('selectionChanged.chart', draw);
project.on('trackChanged.chart', trackChanged);
this.$chart = this.$el.find('[data-name=chartDiv]');
var $dialog = $('<div style="background:white;" title="Chart"></div>');
var $configPane = this.$el.find('[data-name=configPane]');
formBuilder.$form.appendTo($configPane);
this.$el.appendTo($dialog);
$dialog.dialog({
close: function (event, ui) {
project.off('trackChanged.chart', trackChanged);
project.getRowSelectionModel().off('selectionChanged.chart', draw);
project.getColumnSelectionModel().off('selectionChanged.chart',
draw);
_this.$el.empty();
},
resizable: true,
height: 600,
width: 900
});
this.$dialog = $dialog;
this.draw();
};
morpheus.PcaPlotTool.getVectorInfo = function (value) {
var field = value.substring(0, value.length - 2);
var isColumns = value.substring(value.length - 2) === '_c';
return {
field: field,
isColumns: isColumns
};
};
morpheus.PcaPlotTool.prototype = {
annotate: function (options) {
var _this = this;
var formBuilder = new morpheus.FormBuilder();
formBuilder.append({
name: 'annotation_name',
type: 'text',
required: true
});
formBuilder.append({
name: 'annotation_value',
type: 'text',
required: true
});
morpheus.FormBuilder
.showOkCancel({
title: 'Annotate Selection',
content: formBuilder.$form,
okCallback: function () {
var dataset = options.dataset;
var eventData = options.eventData;
var array = options.array;
var value = formBuilder.getValue('annotation_value');
var annotationName = formBuilder
.getValue('annotation_name');
// var annotate = formBuilder.getValue('annotate');
var isRows = true;
var isColumns = true;
var existingRowVector = null;
var rowVector = null;
if (isRows) {
existingRowVector = dataset.getRowMetadata()
.getByName(annotationName);
rowVector = dataset.getRowMetadata().add(
annotationName);
}
var existingColumnVector = null;
var columnVector = null;
if (isColumns) {
existingColumnVector = dataset.getColumnMetadata()
.getByName(annotationName);
columnVector = dataset.getColumnMetadata().add(
annotationName);
}
for (var p = 0, nselected = eventData.points.length; p < nselected; p++) {
var item = array[eventData.points[p].pointNumber];
if (isRows) {
if (_.isArray(item.row)) {
item.row.forEach(function (r) {
rowVector.setValue(r, value);
});
} else {
rowVector.setValue(item.row, value);
}
}
if (isColumns) {
columnVector.setValue(item.column, value);
}
}
if (isRows) {
morpheus.VectorUtil
.maybeConvertStringToNumber(rowVector);
_this.project.trigger('trackChanged', {
vectors: [rowVector],
render: existingRowVector != null ? []
: [morpheus.VectorTrack.RENDER.TEXT],
columns: false
});
}
if (isColumns) {
morpheus.VectorUtil
.maybeConvertStringToNumber(columnVector);
_this.project.trigger('trackChanged', {
vectors: [columnVector],
render: existingColumnVector != null ? []
: [morpheus.VectorTrack.RENDER.TEXT],
columns: true
});
}
}
});
},
draw: function () {
var _this = this;
this.$chart.empty();
var plotlyDefaults = morpheus.ChartTool.getPlotlyDefaults();
var layout = plotlyDefaults.layout;
var config = plotlyDefaults.config;
var chartWidth = 400;
var chartHeight = 400;
var showPoints = this.formBuilder.getValue('show_points');
var groupColumnsBy = this.formBuilder.getValue('group_columns_by');
var axisLabel = this.formBuilder.getValue('axis_label');
var colorBy = this.formBuilder.getValue('color');
var sizeBy = this.formBuilder.getValue('size');
var groupRowsBy = this.formBuilder.getValue('group_rows_by');
var dataset = this.project.getSelectedDataset({
emptyToAll: false
});
this.dataset = dataset;
if (dataset.getRowCount() * dataset.getColumnCount() === 0 || dataset.getRowCount() != 2) {
$('<h4>Please select 2 rows and any number of columns in the heat map.</h4>')
.appendTo(this.$chart);
return;
}
if ((dataset.getRowCount() * dataset.getColumnCount()) > 100000) {
showPoints = false;
}
var project = this.project;
var expressionSet = project.getFullDataset().getESSession();
var columnIndices = dataset.columnIndices;
var rowIndices = dataset.rowIndices;
var req = ocpu.call("pcaPlot", {
es : expressionSet,
columns : columnIndices,
c1 : rowIndices[0],
c2 : rowIndices[1],
colour : colorBy,
size : sizeBy
}, function (session) {
var img = $('<img />', {src : session.getLoc() + 'graphics/1/png'});
_this.$chart.append(img);
});
req.fail(function () {
alert("failed to create pcaPlot");
})
}
};
src/ui/heat_map_toolbar.js
View file @ e599771c
......@@ -253,11 +253,8 @@ morpheus.HeatMapToolBar = function (controller) {
$buttons.on('click', '[name=pca]', function () {
console.log("test button clicked");
new morpheus.PcaPlotTool({
project: controller.getProject(),
getVisibleTrackNames: _.bind(
controller.getVisibleTrackNames, controller)
});
new morpheus.PcaPlotTool({project : controller.getProject()});
});
var $lineOneColumn = $el.find('[data-name=lineOneColumn]');
......
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