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<!DOCTYPE html>
<meta charset="utf-8">
<link rel="stylesheet" href="http://apps.neotomadb.org/dojo/1.10.4/dijit/themes/claro/claro.css"/>
<link rel="stylesheet" href="./stratigraphic.css" />
<body class="claro">
<h1>Stratigraphic API Plots - Tester</h1>
<div class="demo-controls-container data-selection">
<h2>Select Dataset Type and Dataset ID</h3>
<div class="control-row">
<label for="fsDataType">Select data type:</label>
<select data-dojo-type="dijit/form/FilteringSelect"
data-dojo-props="searchAttr: 'value', placeHolder:'select dataset type', promptMessage: 'Type or select dataset type'"
id="fsDataType" name="fsDataTypes" >
<option value="pollen">pollen</option>
<option value="ostracode">ostracode</option>
<option value="diatom">diatom</option>
<option value="vertebrate fauna" >vertebrate fauna</option>
</select>
</div>
<div class="control-row">
<label for="fsDatasetID">Dataset Id:</label>
<div data-dojo-type="dijit/form/FilteringSelect" id="fsDatasetID" data-dojo-props="searchAttr:'DatasetID', placeHolder:'select dataset id', autoComplete: true, required: false, maxHeight: 200">
</div>
</div>
<div class="dataset-metadata"></div>
</div>
<h2 class="diagram-heading">Stratigraphic Diagram</h2>
<h3 id="label-site-dataset"></h3>
<div class="taxa-labels"></div>
<div class="charts"></div>
<h2 id="demo-controls-label">Demo controls:</h2>
<div id="left-col">
<div class="demo-controls-container chart-filter">
<h4 id="demo-controls-description">Filter and Group Data</h4>
<div class="control-row">
<label for="genusGroup">Enter genus to group by (separate with ";"):</label>
<input type="text" name="firstname" value=""
data-dojo-type="dijit/form/TextBox"
data-dojo-props="placeHolder:'Enter genus, separate with ;'" id="genusGroup" />
</div>
<div class="control-row">
<label for="fsVariableUnit">Variable Unit:</label>
<select data-dojo-type="dijit/form/FilteringSelect" id="fsVariableUnits" data-dojo-props="searchAttr:'VariableUnits', placeHolder:'select variable units', autoComplete: true, required: false"></select>
</div>
<div class="control-row">
<label for="topxSpinner">Top Taxa:</label>
<input data-dojo-type="dijit/form/NumberSpinner"
id="topxSpinner"
value="10"
style="width:42px"
data-dojo-props="smallDelta:1, constraints:{min:5,max:15,places:0},intermediateChanges:true"
name="topxSpinner">
</div>
<div class="control-row">
<button data-dojo-type="dijit/form/Button" id="btnApplyFilterAndGroup">Apply Filter & Group Settings</button>
</div>
</div>
<div class="demo-controls-container chart-filter" id="interactionForm" data-dojo-type="dijit/form/Form">
<h4>Chart Interaction</h4>
<div class="control-row">
<div data-dojo-type="dojo/store/Memory"
data-dojo-id="yAxisStore"
data-dojo-props="data: [{DomainName: 'Depth', ChronologyID: null, UnitType: 'Depth' }]">
</div>
<label for="fsSelectYaxis">Y Axis: </label>
<div data-dojo-type="dijit/form/FilteringSelect" id="fsSelectYAxis" data-dojo-props="searchAttr: 'DomainName', placeHolder:'select y axis domain', promptMessage: 'Type or select chronology or depth'">
</div>
</div>
<div class="control-row">
<label for="chartTypeForm">Select Chart Type:</label>
<form id="chartTypeForm" style="display:inline;" name="chartTypeForm" >
<input data-dojo-type="dijit/form/RadioButton" name="chartTypeRadioButtons" data-lpignore="true" id="radioFilledArea" name="chartType" value="FilledArea" >
<label for="radioFilledArea">Filled Area</label>
<input data-dojo-type="dijit/form/RadioButton" name="chartTypeRadioButtons" data-lpignore="true" id="radioBarChart" name="chartType" value="BarChart">
<label for="radioBarChart">Bar Chart</label>
<input data-dojo-type="dijit/form/RadioButton" name="chartTypeRadioButtons" data-lpignore="true" id="radioSymbolPlot" name="chartType" value="SymbolPlot">
<label for="radioSymbolPlot">Symbol Plot</label>
</form>
</div>
<div class="area-controls control-row">
<label for="showExaggeration">Show 5x Exaggeration</label>
<input type="checkbox" id ="showExaggeration" checked="true">
</div>
</div>
</div>
<div id="right-col">
<div id="legend">
<h4 class="legend-title">Ecology Group ID</h4>
<div class="legend-container"></div>
</div>
</div>
</body>
<link rel="stylesheet" href="./stratigraphic.css" />
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/4.6.0/d3.min.js" charset="utf-8"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/d3-queue/3.0.3/d3-queue.min.js"></script>
<script src="https://d3js.org/d3-request.v1.min.js"></script>
<script>
var appRoot = "/stratigraphic-plot-pollen/";
var dojoConfig = {
isDebug: 1,
async: 1,
};
</script>
<script src="//apps.neotomadb.org/dojo/1.10.4/dojo/dojo.js"></script>
<script src="./js/sd-data-retrieval.js" ></script>
<script src="./js/sd-tester-ui.js" ></script>
<script src="./js/sd-model.js" ></script>
<script type="text/javascript">
var busy;
var topic;
var fsbusy;
var initialized = false;
require(["dojo/parser", "dijit/registry", "dojo/store/Memory", "dojo/request/xhr", "dojox/widget/Standby", "dojo/topic", "dojo/on", "dojo/dom", "dojo/query", "dijit/layout/BorderContainer", "dijit/layout/ContentPane", "dijit/form/FilteringSelect", "dijit/layout/ContentPane", "dijit/form/RadioButton", "dojo/domReady!"],
//omit "neotoma/form/StratigraphicDiagram",
function (parser, registry, Memory, xhr, Standby, ltopic, on, dom, query) {
/*set globals*/
topic = ltopic;
parser.parse().then(
function () {
/*
// cache diagrammer
dojo.config.diagrammer = registry.byId("diagrammer");
if (dojo.config.diagrammer == null) {
alert("Can't find diagrammer.");
return;
}
// initialize chronologies
dojo.config.diagrammer.chronologies = [];
*/
// set up standby
var chartContainer = query(".charts")[0];
busy = new Standby({ target: chartContainer });
document.body.appendChild(busy.domNode);
busy.startup();
// listen to show and hide busy Standby
topic.subscribe("diagrammer/ShowStandby",
function () {
busy.show();
}
);
topic.subscribe("diagrammer/HideStandby",
function () {
busy.hide();
}
);
//clear parsed filteringselect
//clearDatasetType();
bindListeners();
instantiateFSBusy();
/*
//get default dataset type ids
var defaultDSType;
var dijitfsDataType = dijit.registry.byId("fsDataType");
if(dijitfsDataType){
defaultDSType = dijitfsDataType.get("value");
}
if(defaultDSType){
xhr.get("http://api.neotomadb.org/v1/data/datasets?datasettype="+defaultDSType,
{
handleAs: "json",
headers: {
"X-Requested-With": null
}
}
).then(
function (response) {
if (response.success === 1) {
var datasetIds = registry.byId("fsDatasetID");
datasetIds.set("store",
new Memory(
{
idProperty: "DatasetID",
data: response.data
}
)
);
} else {
alert("Error getting pollen datasetids");
}
},
function (response) {
console.log("Error on server loading pollen datasets: " + response);
}
);
}
END skip load default datatype
*/
//TESTING
//load local dataset
setDefaultSelection();
},
function (err) {
alert("error parsing");
}
);//end parse
});//end require
/*
d3.request("http://api.neotomadb.org/v1/data/Downloads/17723?)
//.header("X-Requested-With", "XMLHttpRequest")
//.header("Content-Type", "application/x-www-form-urlencoded")
//.post("a=2&b=3", callback);
*/
/*GLOBAL VARS */
var plot_size = {h: 280, w: 300};
var chartIntervalWidth = 8;
var fixedWidth = 50;
var chartGapLeft = 5;
var chartGapRight = 12;
var margin = {top: 15, right: 50, bottom: 28, left: 80};
var longLabelHeight = 150;
var width = plot_size.w - margin.left - margin.right,
height = plot_size.h - margin.top - margin.bottom;
var strataYScale, strataXScale, yAxis,
sampleData, SampleIDMap, summaryDataBySampleID, currentChronologyName, taxaRenderObjects,
sortedtaxaRenderObjects, metadata, handlerChangeDatasetID, handlerChangeDatasetType;
//var currentTopX = 10;
var tooltip = d3.select("body").append("div")
.attr("class", "tooltip")
.style("opacity", 0);
//color scheme
var colors20 = d3.scaleOrdinal(d3.schemeCategory10);
var colorMap = {
"TRSH": "#877F13",
"UPHE": "#C4A64D",
"VACR": "#BF3E21",
"BNTH": "#313695",
"NEKT": "#3f007d",
"DIAT": "#EC7014"
};
var taxaline, taxaarea, taxaline5x, taxaarea5x, yAxisParameter, currentDatasetType;
var defaultDatasetID = 7685;//17851;//17723;
function instantiateFSBusy(){
require(["dojo/query","dojox/widget/Standby", "dojo/topic"],function(query, Standby,topic){
var fsFacade = query("#widget_fsDatasetID")[0];
fsbusy = new Standby({ target: fsFacade });
document.body.appendChild(fsbusy.domNode);
fsbusy.startup();
// listen to show and hide busy Standby
topic.subscribe("datasetselect/ShowStandby",
function () {
fsbusy.show();
}
);
topic.subscribe("datasetselect/HideStandby",
function () {
fsbusy.hide();
}
);
});
}
function apiDownloadDataset(datasetid){
d3.json("http://api.neotomadb.org/v1/data/Downloads/"+datasetid+"?", handleResult);
//.mimeType("application/json")
//.get(handleResult);
}
function setDefaultSelection(){
require(["dijit/registry","dojo/on", "dojo/dom"],function(registry,on,dom){
//set dataset type fs
var fsDatasetType = registry.byId("fsDataType");
fsDatasetType.set("value","vertebrate fauna");
var dijitRBSymbolPlot = registry.byId("radioSymbolPlot");
var dijitRBBarChart = registry.byId("radioBarChart");
var dijitRBFilledArea = registry.byId("radioFilledArea");
var toggle5xControl = dom.byId("showExaggeration");
var yAxisSelect = registry.byId("fsSelectYAxis");
var topxSpinner = registry.byId("topxSpinner");
var groupGenus = registry.byId("genusGroup");
var fsVarUnit = registry.byId("fsVariableUnits");
dijitRBFilledArea.set("selected",true);
fsVarUnit.set("value","NISP");
});
}
function filterEcolGroup(){
}
function showAll(){
}
function defineNumericRenderers(){
}
function updateChartTitle(dataset){
var h3 = d3.select("#label-site-dataset")
.html("Site: "+dataset.Site.SiteName+" | DatasetID: "+dataset.DatasetID);
}
function handleResult(err, result){
topic.publish("diagrammer/HideStandby");
if(err){
console.log("Error with request");
return;
}
var dataset = result.data[0];//.response;
updateChartTitle(dataset);
processData(dataset,function(){
//processData callback
//set values
setVariableUnit();
setDefaultChartType();
updateYAxisFilteringSelect();
//set yscale
setYLookupFunction(metadata.yAxisDomainName);//or with defChronolgyID get defChronologyName
updateVariableUnitFilteringSelect(metadata.allVarUnits);
//set var. unit fs
updateVariableUnitUI();
prepareUI(function(){
//create renderObjects
taxaRenderObjects = createTaxaObjectsToRenderAsChart(metadata.variableUnit);
//prepareUI callback
sortedtaxaRenderObjects = sortFilterData(taxaRenderObjects);
//renderData();
renderNewData(sortedtaxaRenderObjects);
initialized = true;
});
});
//prepareUI();
//renderData(taxaRenderObjects);
}
function updateChart(){
//case#1: VariableUnit changes
taxaRenderObjects = createTaxaObjectsToRenderAsChart(metadata.variableUnit);
//prepareUI callback
sortedtaxaRenderObjects = sortFilterData(taxaRenderObjects);
//renderData();
renderNewData(sortedtaxaRenderObjects);
}
//programmatically update Var.Unit UI
function updateVariableUnitUI(){
if(metadata.variableUnit){
//prevent handler from reponsding to FS change event
handlerChangeVariableUnit.remove();
require(["dijit/registry","dojo/on"],function(registry,on){
var fsVU = registry.byId("fsVariableUnits");
fsVU.set("value",metadata.variableUnit);
//enable fs change handler
handlerChangeVariableUnit = on(fsVU, "change", handleVariableUnitChange);
})
}
}
function updateYAxisFilteringSelect(){
require(["dojo/store/Memory", "dijit/registry", "dojo/on"],function(Memory, registry,on){
//get filteringselect
var yaxisfs = registry.byId("fsSelectYAxis");
//selection store
var ageDepthStore = [];
ageCollection.forEach(function(d){
if(!d.ValidAge){
//omit from fs; can't use
return;
}
var storeObj = {};
storeObj.ChronologyID = d.ChronologyID;
storeObj.DomainName = d.ChronologyName;
storeObj.UnitType = "Age";
ageDepthStore.push(storeObj);
})
//create depth store object if Depth values exist
//some fauna have no depth
if(metadata.depthCollection.DepthExtent[0]){
var storeObj = {};
storeObj.ChronologyID = null;
storeObj.DomainName = "Depth";
storeObj.UnitType = "Depth";
ageDepthStore.push(storeObj);
}
//update memory with newly created ageCollection
yAxisStore = new Memory({data: ageDepthStore, idProperty: "DomainName"});
yaxisfs.set("store", yAxisStore);
})
}
function setMetaData(property, value){
metadata[property] = value;
}
function clearMetaData(){
//clear all references
metadata = {};
}
//define valid pollen EcolGroupIDs
function pollenEcolGroupIDFilter(dataset){
//TO DO: take user input for ecolgroupids
var includeEcolGroupIDs = ["TRSH","UPHE","VACR"];
var filteredDataset = [];
var filteredSamples = [];
var filteredSamples = dataset.Samples;
filteredSamples.forEach(function(d){
var filteredSampleData = [];
filteredSampleData = d.SampleData.filter(function(e){
return includeEcolGroupIDs.indexOf(e.EcolGroupID) > -1;
})
d.SampleData = filteredSampleData;
});
//variables byRef so can simpley return dataset as altered object; filteredSamples and dataset.Samples reference the same object
filteredDataset = dataset;
filteredDataset.Samples = filteredSamples;
return filteredDataset;
}
function processData(dataset,callback){
/**get useful dataset metadata
* dataset.DatasetID: id
* dataset.DefChronologyID: default chronologyid
* dataset.DOI
* dataset.Site.SiteName
* dataset.Site.SiteID
* dataset.DatasetType
*/
metadata = {};
metadata.datasetType = dataset.DatasetType;
metadata.chartTypeSelection = null;
metadata.yAxisDomainName = null;
metadata.yAxisLabel = null;
metadata.yAxisUnitType = null;
metadata.yAxisDomainExtent = [];
metadata.yAxisAgeLookupFunction = null;
metadata.currentTopX = 10;
setMetaData("DefChronologyID", dataset.DefChronologyID);
//metadata.DefChrongologyID = dataset.DefChronologyID;
//filter for EcolGroupID(s) of interest
switch(metadata.datasetType){
case "pollen":
//currently include only UPHE, TRSH, VACR
dataset = pollenEcolGroupIDFilter(dataset);
break;
case "ostracode":
//no EcolGroupID filter
break;
case "vertebrate fauna":
//no EcolGroupID filter
break;
case "diatom":
//no EcolGroupID filter
break;
}
//get set of unique SampleID values
var SampleIDs = d3.set(dataset.Samples, function(d){
return "S"+d.SampleID;
}).values();
//create map of SampleID, Depth
var sampleDepths;
sampleDepths = d3.map();
dataset.Samples.forEach(function(d){
sampleDepths.set("S"+d.SampleID, d.AnalysisUnitDepth);
});
var depthExtent;
depthExtent = d3.extent(sampleDepths.values());
var depthCollection = {};
depthCollection.DepthExtent = depthExtent;
depthCollection.DepthLookup = sampleDepths;
depthCollection.Units = "cm";
metadata.depthCollection = depthCollection;
//create ageCollection of SampleID, Age maps for each chronology
ageCollection = [];
dataset.Samples[0].SampleAges.forEach(function(d){
var ageObj = {};
ageObj.AgeType = d.AgeType;
ageObj.ChronologyID = d.ChronologyID;
ageObj.ChronologyName = d.ChronologyName;
ageObj.AgeExtent = [];
ageObj.AgeLookup = d3.map();
ageCollection.push(ageObj);
});
//extract and concatenate SampleData object arrays into sampleData
//{}8 properties: TaxonName, VariableUnits, VariableElement, VariableContext, TaxaGroup, Value, EcolGroupID, + SampleID
sampleData = [];
var ageData = [];
dataset.Samples.forEach(function(d,i){
var theSampleID = "S"+d.SampleID;
d.SampleData.forEach(function(e,j){
e.SampleID = theSampleID;
})
d.SampleAges.forEach(function(f,k){
f.SampleID = theSampleID;
})
sampleData = sampleData.concat(d.SampleData);
ageData = ageData.concat(d.SampleAges);
})
//extract unique values for VariableUnits, TaxonName, EcolGroupID
var allVarUnits = [];
allVarUnits = d3.set(sampleData,function(d){return d.VariableUnits}).values();
metadata.allVarUnits = allVarUnits;
/**Set Defaults: round 1
variableUnit, chartType, topX, genusGrouping
**/
//set default variableUnit
//setVariableUnit();
//setDefaultChartType();
var allTaxaNames = [];
allTaxaNames = d3.set(sampleData,function(d){return d.TaxonName}).values();
metadata.allTaxaNames = allTaxaNames;
metadata.allEcolGroupIDs = d3.set(sampleData,function(d){return d.EcolGroupID}).values();
//all possible y axis scales {Depth, ChronID#1, ChronID#2, ...}
ageCollection.forEach(function(d){
var theAge = d.ChronologyID;
var sampleAges = d3.map();
var currentAgeData = ageData.filter(function(e){
return e.ChronologyID = theAge;
})
currentAgeData.forEach(function(f){
//sampleAges.set(d.SampleID, d.Age);
//test vertebrate fauna w/ only youngestAge, oldestAge
var ageObj = {};
ageObj.AgeYounger = f.AgeYounger;
ageObj.Age = f.Age;
ageObj.AgeOlder = f.AgeOlder;
ageObj.AgeMean = null;
if(f.AgeYounger != NaN && f.AgeOlder != NaN){
ageObj.AgeMean = (f.AgeYounger + f.AgeOlder)/2;
}
sampleAges.set(f.SampleID, ageObj);
});
//any of the age values may be null
var arrAllAgeValues = [];
sampleAges.each(function(g){
arrAllAgeValues.push(g.AgeYounger);
arrAllAgeValues.push(g.Age);
arrAllAgeValues.push(g.AgeOlder);
})
var ageExtent = d3.extent(arrAllAgeValues);
d.AgeLookup = sampleAges;
d.AgeExtent = ageExtent;
//test always true
d.ValidAge = true;
//validate AgeExtent
if ((d.AgeExtent[1] - d.AgeExtent[0]) >= 0){
d.ValidAge = true
}
if (d.AgeExtent[0] == null || d.AgeExtent[1] == null){
d.ValidAge = false;
}
})
metadata.ageCollection = ageCollection;
//set initial yLookupFunction
if(metadata.ageCollection[0].ValidAge){
metadata.yAxisAgeLookupFunction = metadata.ageCollection[0].AgeLookup;
metadata.yAxisDomainName = metadata.ageCollection[0].ChronologyName;
metadata.yAxisUnitType = "Age";
} else {
metadata.yAxisAgeLookupFunction = metadata.depthCollection.DepthLookup;
metadata.yAxisDomainName = "Depth";
metadata.yAxisUnitType = "Depth";
}
//todo add getter/setter for ageCollection
//updateYAxisFilteringSelect();
//updateVariableUnitFilteringSelect(allVarUnits);
//get summary stats by SampleID for topX selection, abundance calculation
var dataBySampleID = d3.nest()
.key(function(d){
return d.SampleID;
})
.key(function(d){
return d.VariableUnits;
})
//.rollup(function(values){
// return {
// totalCount: d3.sum(values, function(d){ return d.value})
//}
//})
.map(sampleData);
summaryDataBySampleID = d3.nest()
.key(function(d){
return d.SampleID;
})
.key(function(d){
return d.VariableUnits;
})
.rollup(function(values){
var currentKey = values[0].VariableUnits;//JSON.stringify(values);
switch(currentKey){
case "NISP":
return {
sumNISP: d3.sum(values, function(d){ return d.Value}),
countTaxa: values.length
}
break;
case "valves/g":
return {
meanConcentration: d3.mean(values, function(d){ return d.Value})
}
break;
case "MNI":
return {
sumMNI: d3.sum(values, function(d){ return d.Value})
}
break;
case "present/absent":
return {
countTaxa: values.length
}
break;
default:
return {
countTaxa: values.length
}
break;
}
})
.map(sampleData);
//taxaRenderObjects = createTaxaObjectsToRenderAsChart(metadata.variableUnit);
callback();
}
function sortFilterData(srcTaxaRenderObjects){
//sort taxa value collections by abundance
abundTaxaRenderObjects = srcTaxaRenderObjects.sort(sortAbundanceDesc);
//then by Age within taxa value collections if not showing depth
if(metadata.yAxisUnitType == "Age"){
abundTaxaRenderObjects.forEach(function(d){
var vals = d.values;
var sortedValues = vals.sort(sortByAgeYounger);
d.values = sortedValues;
})
}
var topXtaxaRenderObjects = filterForTopX(abundTaxaRenderObjects, metadata.currentTopX);
//createEcolGroupRenderObjects()
var bottomNtaxaRenderObjects = filterForBottomN(abundTaxaRenderObjects, metadata.currentTopX);
//group bottomN by EcolGroupID
//see Line 655
//var groupedTaxa = groupByEcolGroupID(bottomNtaxaRenderObjects, "NISP");
var groupedTaxa = groupByEcolGroupID(bottomNtaxaRenderObjects, metadata.variableUnit);
var sortedtaxaRenderObjects = topXtaxaRenderObjects.sort(sortEcolGroupThenTaxonName);
//append grouped data to taxa data
var aggregatedRenderObjects = sortedtaxaRenderObjects.concat(groupedTaxa);
return aggregatedRenderObjects;
}
function renderDataOld(){
sortedtaxaRenderObjects.forEach(function(d,i){
constructChart(d,i);
});
}
function sortSampleID(a,b){
var x = +a.SampleID.substr(1,a.SampleID.length);
var y = +b.SampleID.substr(1,b.SampleID.length);
return x - y;
}
function sortByAgeYounger(a,b){
//get AgeYounger
var x = lookupYValueBySampleID(a.SampleID);
var y = lookupYValueBySampleID(b.SampleID);
return x - y;
}
//sort by maxAbundance
function sortAbundanceDesc(a,b){
var x = a.maxAbundance;
var y = b.maxAbundance;
return x < y ? 1 : x > y ? -1 : 0;
}
//get key: , maxAbundance
//filter for TopX
function filterForTopX(theArray,x){
var result = theArray.filter(function(d,i){
return i < x;
})
return result;
}
function filterForBottomN(theArray, x){
var result = theArray.filter(function(d,i){
return i >= x;
})
return result;
}
//sort again by EcolGroupID, then TaxonName
function sortEcolGroupThenTaxonName(a,b){
if(a.EcolGroupID == b.EcolGroupID){
var x = a.key;
var y = b.key;
return x < y ? -1 : x > y ? 1 : 0;
}
var x = a.EcolGroupID;
var y = b.EcolGroupID;
return x < y ? -1 : x > y ? 1 : 0;
}
function groupByEcolGroupID(theArray, variableUnit){
//for each allEcolGrooupIDs[]
var ecoGrpRenderObjects = [];
metadata.allEcolGroupIDs.forEach(function(d){
var obj = {};
obj.EcolGroupID = d;
obj.values = [];
ecoGrpRenderObjects.push(obj);
});
//for each groupID, get all samples, aggregate by SampleID
ecoGrpRenderObjects.forEach(function(d){
var filteredByEcoGrp = theArray.filter(function(e){
return e.EcolGroupID === d.EcolGroupID;
})
//append all values objects to EcolGroup collection
filteredByEcoGrp.forEach(function(f){
//concatenate arr of objects
var tmpArr = d.values.concat(f.values);
//replace with result of concatenation
d.values = tmpArr;
})
});
//now sum values
//want:
/**{}
.EcolGroupID
.key
.maxAbundance
.values:[]
.EcolGroupID
.SampleID
.Value
.VariableUnits
.Abundance
//have:
.EcolGroupID
.values[]
**/
//for leftover taxa not in top group
//aggregate values by SampleID by EcolGroupID
ecoGrpRenderObjects.forEach(function(d){
//for each EcolGroupID, total values by SampleID across all taxa
var nest = d3.nest().key(function(e){
return e.SampleID })
.rollup(function(values){
return {
//sum of values across taxa within shared EcolGroupID at SampleID
totalValue: d3.sum(values, function(f){
return f.Value})
}
})
.map(d.values);
//for each EcolGroupID, generate a display object aggregating properties for each SampleID
d.key = "Other "+d.EcolGroupID;
d.values = [];
nest.each(function(value, key){
var obj = {}
obj.SampleID = key;
//compare to value at SampleID in summaryDataBySampleID
var sampleAggregate = getSampleAggregateByVariableUnit(key,value.totalValue);
if(sampleAggregate){
obj.Value = sampleAggregate;
} else {
obj.Value = null;
}
obj.EcolGroupID = d.EcolGroupID;
d.values.push(obj);
});
})
//create EcolGroupID lengend objects
createLegend(ecoGrpRenderObjects);
//now calc relative abundance
ecoGrpRenderObjects.forEach(function(d){
d.values.forEach(function(e){
e.Abundance = (e.Value/summaryDataBySampleID.get(e.SampleID).get(variableUnit).sumNISP)*100;
})
var abundanceExtent = d3.extent(d.values,function(f){
return f.Abundance;
});
var valueExtent = d3.extent(d.values, function(f){
return f.Value;
})
if(abundanceExtent){
d.maxAbundance = abundanceExtent[1];
} else {
console.log("Error calculating maxAbundance");
d.maxAbundance = 0;
}
if(valueExtent){
d.maxValue = valueExtent[1];
} else {
console.log("Error calculating maxValue");
d.maxValue = 0;
}
})
//drop objects with no data
var nonNullEcoGrpRenderObjects = ecoGrpRenderObjects.filter(function(d){
return d.values.length > 0;
})
//insure samples are sorted ascending
//if Vertebrate Fauna, order by AgeYounger-- samples are not in chronological order
if(metadata.datasetType == "vertebrate fauna"){
//order by age, not sampleid
nonNullEcoGrpRenderObjects.forEach(function(d){
d.values = d.values.sort(sortByAgeYounger);
})
} else {
nonNullEcoGrpRenderObjects.forEach(function(d){
d.values = d.values.sort(sortSampleID);
})
}
return nonNullEcoGrpRenderObjects;
}
//given current VariableUnit, how should EcolGroupID aggregated sample values be presented?
function getSampleAggregateByVariableUnit(sampleid, value){
var currentVariableUnit = metadata.variableUnit;
var aggValue = null;
switch(currentVariableUnit){
case "NISP":
if(summaryDataBySampleID.get(sampleid).get(currentVariableUnit).sumNISP > 0){
aggValue = (value/summaryDataBySampleID.get(sampleid).get(currentVariableUnit).sumNISP) * 100;
}
break;
case "MNI":
aggValue = value;//summaryDataBySampleID.get(sampleid).get(currentVariableUnit).sumMNI;
break;
case "present/absent":
aggValue = value;//summaryDataBySampleID.get(sampleid).get(currentVariableUnit).present;
break;
default:
console.log("Error returning aggregate value for variable unit/sampleid/ecolgroupid");
break;
}
return aggValue;
}
var symbolRenderer = d3.symbol().size(32).type(d3.symbolCross);
/*
var symbolRenderer = function(){
var symFunc;
//placeholder for cases to be defined
symFunc = d3.symbol().size(32).type(d3.symbolTriangle);
//symFunc = d3.symbol().size(32).type(d3.symbolCross);
return symFunc;
}
*/
//function will generate collection of objects to render
//for each Taxa by chosen VariableUnit
function createTaxaObjectsToRenderAsChart(variableUnit){
//for each VariableUnit
//create dataByTaxaToRender
/*
1. group by taxonname
2. calc abundance value
*/
var varUnitFilteredSamples = sampleData.filter(function(d){
return d.VariableUnits == variableUnit;
})
var filteredTaxaRenderObjects = d3.nest()
.key(function(d){
return d.TaxonName
})
.entries(varUnitFilteredSamples);