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group_dwi.html
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group_dwi.html
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<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta charset="UTF-8">
<title></title>
<style type="text/css">
/* Hide data table */
.csvdata {
display: none;
}
body {
font-family: helvetica;
}
.text-warning {
font-weight: bold;
color: red;
}
/*Primary Chart*/
/*Nested divs for responsiveness*/
.chart-wrapper {
max-width: 800px; /*Overwritten by the JS*/
min-width: 160px;
margin-bottom: 20px;
font-family: helvetica;
}
.chart-wrapper .inner-wrapper {
position: relative;
padding-bottom: 50%; /*Overwritten by the JS*/
width: 100%;
}
.chart-wrapper .outer-box {
position: absolute;
top: 0;
bottom: 0;
left: 0;
right: 0;
}
.chart-wrapper .inner-box {
width: 100%;
height: 100%;
}
.chart-wrapper text {
font-family: helvetica;
font-size: 13px;
}
.chart-wrapper .axis path,
.chart-wrapper .axis line {
fill: none;
stroke: #888;
stroke-width: 2px;
shape-rendering: crispEdges;
}
.chart-wrapper .y.axis .tick line {
stroke: lightgrey;
opacity: 0.6;
stroke-dasharray: 2,1;
stroke-width: 1;
shape-rendering: crispEdges;
}
.chart-wrapper .x.axis .domain {
display: none;
}
.chart-wrapper div.tooltip {
position: absolute;
text-align: left;
padding: 3px;
font-size: 12px;
background: #eee;
border: 0px;
border-radius: 1px;
pointer-events: none;
opacity: .7;
z-index: 10;
}
/*Box Plot*/
.chart-wrapper .box-plot .box {
fill-opacity: .5;
stroke-width: 2;
}
.chart-wrapper .box-plot line {
stroke-width: 2px;
}
.chart-wrapper .box-plot circle {
fill: white;
stroke: black;
}
.chart-wrapper .box-plot .median {
stroke: black;
}
.chart-wrapper .box-plot circle.median {
/*the script makes the circles the same color as the box, you can override this in the js*/
fill: white !important;
}
.chart-wrapper .box-plot .mean {
stroke: white;
stroke-dasharray: 2,1;
stroke-width: 1px;
}
@media (max-width:500px){
.chart-wrapper .box-plot circle {display: none;}
}
/*Violin Plot*/
.chart-wrapper .violin-plot .area {
shape-rendering: geometricPrecision;
opacity: 0.4;
}
.chart-wrapper .violin-plot .line {
fill: none;
stroke-width: 2px;
shape-rendering: geometricPrecision;
}
/*Notch Plot*/
.chart-wrapper .notch-plot .notch {
fill-opacity: 0.4;
stroke-width: 2;
}
/* Point Plots*/
.chart-wrapper .points-plot .point {
/*stroke: black;
stroke-width: 1px;*/
fill-opacity: 0.4;
}
.chart-wrapper .metrics-lines {
stroke-width: 4px;
}
/* Non-Chart Styles for demo*/
.chart-options {
min-width: 200px;
font-size: 13px;
font-family: helvetica;
}
.chart-options button {
margin: 3px;
padding: 3px;
font-size: 12px;
}
.chart-options p {
display: inline;
}
@media (max-width:500px){
.chart-options p {display: block;}
}
</style>
<script type="text/javascript">
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</script>
<script type="text/javascript">
/**
* @fileOverview A D3 based distribution chart system. Supports: Box plots, Violin plots, Notched box plots, trend lines, beeswarm plot
* @version 3.0
*/
/**
* Creates a box plot, violin plot, and or notched box plot
* @param settings Configuration options for the base plot
* @param settings.data The data for the plot
* @param settings.xName The name of the column that should be used for the x groups
* @param settings.yName The name of the column used for the y values
* @param {string} settings.selector The selector string for the main chart div
* @param [settings.axisLabels={}] Defaults to the xName and yName
* @param [settings.yTicks = 1] 1 = default ticks. 2 = double, 0.5 = half
* @param [settings.scale='linear'] 'linear' or 'log' - y scale of the chart
* @param [settings.chartSize={width:800, height:400}] The height and width of the chart itself (doesn't include the container)
* @param [settings.margin={top: 15, right: 60, bottom: 40, left: 50}] The margins around the chart (inside the main div)
* @param [settings.constrainExtremes=false] Should the y scale include outliers?
* @returns {object} chart A chart object
*/
function makeDistroChart(settings) {
var chart = {};
// Defaults
chart.settings = {
data: null,
xName: null,
yName: null,
axisLabels: {xAxis: null, yAxis: null},
labelName: "label",
unitsName: "units",
selector: null,
axisLables: null,
yTicks: 1,
scale: 'linear',
chartSize: {width: 800, height: 400},
margin: {top: 15, right: 10, bottom: 50, left: 50},
constrainExtremes: false,
color: d3.scale.category10(),
modality: null
};
for (var setting in settings) {
chart.settings[setting] = settings[setting]
}
function formatAsFloat(d) {
if (d % 1 !== 0) {
return d3.format(".2f")(d);
} else {
return d3.format(".0f")(d);
}
}
function logFormatNumber(d) {
var x = Math.log(d) / Math.log(10) + 1e-6;
return Math.abs(x - Math.floor(x)) < 0.6 ? formatAsFloat(d) : "";
}
chart.yFormatter = formatAsFloat;
chart.data = chart.settings.data;
iqmName = chart.data[0][chart.settings.xName]
if (iqmName.indexOf('_') > 0) {
iqmName = iqmName.substr(0, iqmName.indexOf('_'))
}
chart.settings.axisLabels.yAxis = iqmName.toUpperCase()
if (iqmName.toLowerCase().startsWith('fd') || iqmName.toLowerCase().startsWith('spikes')) {
chart.settings.constrainExtremes = true
}
units = chart.data[0][chart.settings.unitsName]
if (units) {
chart.settings.axisLabels.yAxis += ' (' + units + ')'
}
chart.groupObjs = {}; //The data organized by grouping and sorted as well as any metadata for the groups
chart.objs = {mainDiv: null, chartDiv: null, g: null, xAxis: null, yAxis: null};
chart.colorFunct = null;
/**
* Takes an array, function, or object mapping and created a color function from it
* @param {function|[]|object} colorOptions
* @returns {function} Function to be used to determine chart colors
*/
function getColorFunct(colorOptions) {
if (typeof colorOptions == 'function') {
return colorOptions
} else if (Array.isArray(colorOptions)) {
// If an array is provided, map it to the domain
var colorMap = {}, cColor = 0;
for (var cName in chart.groupObjs) {
colorMap[cName] = colorOptions[cColor];
cColor = (cColor + 1) % colorOptions.length;
}
return function (group) {
return colorMap[group];
}
} else if (typeof colorOptions == 'object') {
// if an object is provided, assume it maps to the colors
return function (group) {
return colorOptions[group];
}
} else {
return d3.scale.category10();
}
}
/**
* Takes a percentage as returns the values that correspond to that percentage of the group range width
* @param objWidth Percentage of range band
* @param gName The bin name to use to get the x shift
* @returns {{left: null, right: null, middle: null}}
*/
function getObjWidth(objWidth, gName) {
var objSize = {left: null, right: null, middle: null};
var width = chart.xScale.rangeBand() * (objWidth / 100);
var padding = (chart.xScale.rangeBand() - width) / 2;
var gShift = chart.xScale(gName);
objSize.middle = chart.xScale.rangeBand() / 2 + gShift;
objSize.left = padding + gShift;
objSize.right = objSize.left + width;
return objSize;
}
/**
* Adds jitter to the scatter point plot
* @param doJitter true or false, add jitter to the point
* @param width percent of the range band to cover with the jitter
* @returns {number}
*/
function addJitter(doJitter, width) {
if (doJitter !== true || width == 0) {
return 0
}
return Math.floor(Math.random() * width) - width / 2;
}
function shallowCopy(oldObj) {
var newObj = {};
for (var i in oldObj) {
if (oldObj.hasOwnProperty(i)) {
newObj[i] = oldObj[i];
}
}
return newObj;
}
/**
* Closure that creates the tooltip hover function
* @param groupName Name of the x group
* @param metrics Object to use to get values for the group
* @returns {Function} A function that provides the values for the tooltip
*/
function tooltipHover(groupName, metrics) {
var tooltipString = "Group: " + groupName;
tooltipString += "<br\>Max: " + formatAsFloat(metrics.max, 0.1);
tooltipString += "<br\>Q3: " + formatAsFloat(metrics.quartile3);
tooltipString += "<br\>Median: " + formatAsFloat(metrics.median);
tooltipString += "<br\>Q1: " + formatAsFloat(metrics.quartile1);
tooltipString += "<br\>Min: " + formatAsFloat(metrics.min);
return function () {
chart.objs.tooltip.transition().duration(200).style("opacity", 0.9);
chart.objs.tooltip.html(tooltipString)
};
}
function axislabelHover(groupName) {
var tooltipString = "Go to definition of " + groupName;
return function () {
chart.objs.tooltip.transition().duration(200).style("opacity", 1.0);
chart.objs.tooltip.html(tooltipString)
};
}
/**
* Closure that creates the tooltip hover function
* @param groupName Name of the x group
* @param metrics Object to use to get values for the group
* @returns {Function} A function that provides the values for the tooltip
*/
function pointHover(label, value) {
var tooltipString = "Subject: " + label + "<br\>Measure: " + value
return function () {
chart.objs.tooltip.transition().duration(200).style("opacity", 1.0);
chart.objs.tooltip.html(tooltipString)
};
}
/**
* Parse the data and calculates base values for the plots
*/
!function prepareData() {
function calcMetrics(values) {
// Do not reorder in-place
values = values.slice(0).sort(d3.ascending)
var metrics = { //These are the original non�scaled values
max: null,
upperOuterFence: null,
upperInnerFence: null,
quartile3: null,
median: null,
mean: null,
iqr: null,
quartile1: null,
lowerInnerFence: null,
lowerOuterFence: null,
min: null
};
metrics.min = d3.min(values);
metrics.quartile1 = d3.quantile(values, 0.25);
metrics.median = d3.median(values);
metrics.mean = d3.mean(values);
metrics.quartile3 = d3.quantile(values, 0.75);
metrics.max = d3.max(values);
metrics.iqr = metrics.quartile3 - metrics.quartile1;
//The inner fences are the closest value to the IQR without going past it (assumes sorted lists)
var LIF = metrics.quartile1 - (1.5 * metrics.iqr);
var UIF = metrics.quartile3 + (1.5 * metrics.iqr);
for (var i = 0; i <= values.length; i++) {
if (values[i] < LIF) {
continue;
}
if (!metrics.lowerInnerFence && values[i] >= LIF) {
metrics.lowerInnerFence = values[i];
continue;
}
if (values[i] > UIF) {
metrics.upperInnerFence = values[i - 1];
break;
}
}
metrics.lowerOuterFence = metrics.quartile1 - (3 * metrics.iqr);
metrics.upperOuterFence = metrics.quartile3 + (3 * metrics.iqr);
if (!metrics.lowerInnerFence) {
metrics.lowerInnerFence = metrics.min;
}
if (!metrics.upperInnerFence) {
metrics.upperInnerFence = metrics.max;
}
return metrics
}
var current_x = null;
var current_y = null;
var current_row;
// Group the values
for (current_row = 0; current_row < chart.data.length; current_row++) {
current_x = chart.data[current_row][chart.settings.xName];
current_y = chart.data[current_row][chart.settings.yName];
current_label = chart.data[current_row][chart.settings.labelName];
if (chart.groupObjs.hasOwnProperty(current_x)) {
chart.groupObjs[current_x].values.push(current_y);
chart.groupObjs[current_x].labels.push(current_label);
} else {
chart.groupObjs[current_x] = {};
chart.groupObjs[current_x].values = [current_y];
chart.groupObjs[current_x].labels = [current_label];
}
}
for (var cName in chart.groupObjs) {
// chart.groupObjs[cName].values.sort(d3.ascending);
chart.groupObjs[cName].metrics = {};
chart.groupObjs[cName].metrics = calcMetrics(chart.groupObjs[cName].values);
}
}();
/**
* Prepare the chart settings and chart div and svg
*/
!function prepareSettings() {
//Set base settings
chart.margin = chart.settings.margin;
chart.divWidth = chart.settings.chartSize.width;
chart.divHeight = chart.settings.chartSize.height;
chart.width = chart.divWidth - chart.margin.left - chart.margin.right;
chart.height = chart.divHeight - chart.margin.top - chart.margin.bottom;
if (chart.settings.axisLabels) {
chart.xAxisLable = chart.settings.axisLabels.xAxis;
chart.yAxisLable = chart.settings.axisLabels.yAxis;
}
if (chart.settings.scale === 'log') {
chart.yScale = d3.scale.log();
chart.yFormatter = logFormatNumber;
} else {
chart.yScale = d3.scale.linear();
}
if (chart.settings.constrainExtremes === true) {
var fences = [];
for (var cName in chart.groupObjs) {
fences.push(chart.groupObjs[cName].metrics.lowerInnerFence);
fences.push(chart.groupObjs[cName].metrics.upperInnerFence);
}
chart.range = d3.extent(fences);
} else {
chart.range = d3.extent(chart.data, function (d) {return d[chart.settings.yName];});
}
chart.colorFunct = getColorFunct(chart.settings.colors);
// Build Scale functions
chart.yScale.range([chart.height, 0]).domain(chart.range).nice().clamp(true);
chart.xScale = d3.scale.ordinal().domain(Object.keys(chart.groupObjs)).rangeBands([0, chart.width]);
//Build Axes Functions
chart.objs.yAxis = d3.svg.axis()
.scale(chart.yScale)
.orient("left")
.tickFormat(chart.yFormatter)
.outerTickSize(0)
.innerTickSize(-chart.width + (chart.margin.right + chart.margin.left));
chart.objs.yAxis.ticks(chart.objs.yAxis.ticks()*chart.settings.yTicks);
chart.objs.xAxis = d3.svg.axis().scale(chart.xScale).orient("bottom").tickSize(5);
}();
/**
* Updates the chart based on the current settings and window size
* @returns {*}
*/
chart.update = function () {
// Update chart size based on view port size
chart.width = parseInt(chart.objs.chartDiv.style("width"), 10) - (chart.margin.left + chart.margin.right);
chart.height = parseInt(chart.objs.chartDiv.style("height"), 10) - (chart.margin.top + chart.margin.bottom);
// Update scale functions
chart.xScale.rangeBands([0, chart.width]);
chart.yScale.range([chart.height, 0]);
// Update the yDomain if the Violin plot clamp is set to -1 meaning it will extend the violins to make nice points
if (chart.violinPlots && chart.violinPlots.options.show == true && chart.violinPlots.options._yDomainVP != null) {
chart.yScale.domain(chart.violinPlots.options._yDomainVP).nice().clamp(true);
} else {
chart.yScale.domain(chart.range).nice().clamp(true);
}
//Update axes
chart.objs.g.select('.x.axis').attr("transform", "translate(0," + chart.height + ")").call(chart.objs.xAxis)
.selectAll("text")
.attr("y", 5)
.attr("x", -5)
.attr("transform", "rotate(-45)")
.style("text-anchor", "end");
chart.objs.g.select('.x.axis .label').attr("x", chart.width / 2);
chart.objs.g.select('.y.axis').call(chart.objs.yAxis.innerTickSize(-chart.width));
chart.objs.g.select('.y.axis .label').attr("x", -chart.height / 2);
chart.objs.chartDiv.select('svg').attr("width", chart.width + (chart.margin.left + chart.margin.right)).attr("height", chart.height + (chart.margin.top + chart.margin.bottom));
return chart;
};
/**
* Prepare the chart html elements
*/
!function prepareChart() {
// Build main div and chart div
chart.objs.mainDiv = d3.select(chart.settings.selector)
.style("width", chart.divWidth + "px")
.style("display", "inline-block");
// Add all the divs to make it centered and responsive
chart.objs.mainDiv.append("div")
.attr("class", "inner-wrapper")
.style("padding-bottom", (chart.divHeight / chart.divWidth) * 100 + "%")
.append("div").attr("class", "outer-box")
.append("div").attr("class", "inner-box");
// Capture the inner div for the chart (where the chart actually is)
chart.selector = chart.settings.selector + " .inner-box";
chart.objs.chartDiv = d3.select(chart.selector);
d3.select(window).on('resize.' + chart.selector, chart.update);
// Create the svg
chart.objs.g = chart.objs.chartDiv.append("svg")
.attr("class", "chart-area")
.attr("width", chart.width + (chart.margin.left + chart.margin.right))
.attr("height", chart.height + (chart.margin.top + chart.margin.bottom))
.append("g")
.attr("transform", "translate(" + chart.margin.left + "," + chart.margin.top + ")");
// Create axes
chart.objs.axes = chart.objs.g.append("g").attr("class", "axis");
chart.objs.axes.append("g")
.attr("class", "x axis")
.attr("transform", "translate(0," + chart.height + ")")
.call(chart.objs.xAxis);
chart.objs.axes.append("g")
.attr("class", "y axis")
.call(chart.objs.yAxis)
.append("text")
//.attr("class", "label")
.attr("transform", "rotate(-90)")
//.attr("y", -42)
.attr("y", 6)
.attr("dy", ".71em")
//.attr("x", -chart.height / 2)
.style("text-anchor", "end")
.style("font-size", "16px")
.append("a")
.attr("xlink:href", function(d) {
label = chart.yAxisLable.toLowerCase()
charidx = label.indexOf(' ')
if (charidx > 1) { label = label.substr(0, charidx); }
charidx = label.indexOf('_')
if (charidx > 1) { label = label.substr(0, charidx); }
return "http://mriqc.readthedocs.io/en/latest/iqms/" + chart.settings.modality.toLowerCase() + ".html#iqms-" + label
})
.text(chart.yAxisLable)
.on("mouseover", function () {
chart.objs.tooltip
.style("display", null)
.style("left", (d3.event.pageX) + "px")
.style("top", (d3.event.pageY - 28) + "px");
}).on("mouseout", function () {
chart.objs.tooltip.style("display", "none");
}).on("mousemove", axislabelHover(chart.yAxisLable));
// Create tooltip div
chart.objs.tooltip = chart.objs.mainDiv.append('div').attr('class', 'tooltip');
for (var cName in chart.groupObjs) {
chart.groupObjs[cName].g = chart.objs.g.append("g").attr("class", "group");
}
chart.update();
}();
/**
* Render a violin plot on the current chart
* @param options
* @param [options.showViolinPlot=true] True or False, show the violin plot
* @param [options.resolution=100 default]
* @param [options.bandwidth=10 default] May need higher bandwidth for larger data sets
* @param [options.width=50] The max percent of the group rangeBand that the violin can be
* @param [options.interpolation=''] How to render the violin
* @param [options.clamp=0 default]
* 0 = keep data within chart min and max, clamp once data = 0. May extend beyond data set min and max
* 1 = clamp at min and max of data set. Possibly no tails
* -1 = extend chart axis to make room for data to interpolate to 0. May extend axis and data set min and max
* @param [options.colors=chart default] The color mapping for the violin plot
* @returns {*} The chart object
*/
chart.renderViolinPlot = function (options) {
chart.violinPlots = {};
var defaultOptions = {
show: true,
showViolinPlot: true,
resolution: 100,
bandwidth: 20,
width: 50,
interpolation: 'cardinal',
clamp: 1,
colors: chart.colorFunct,
_yDomainVP: null // If the Violin plot is set to close all violin plots, it may need to extend the domain, that extended domain is stored here
};
chart.violinPlots.options = shallowCopy(defaultOptions);
for (var option in options) {
chart.violinPlots.options[option] = options[option]
}
var vOpts = chart.violinPlots.options;
// Create violin plot objects
for (var cName in chart.groupObjs) {
chart.groupObjs[cName].violin = {};
chart.groupObjs[cName].violin.objs = {};
}
/**
* Take a new set of options and redraw the violin
* @param updateOptions
*/
chart.violinPlots.change = function (updateOptions) {
if (updateOptions) {
for (var key in updateOptions) {
vOpts[key] = updateOptions[key]
}
}
for (var cName in chart.groupObjs) {
chart.groupObjs[cName].violin.objs.g.remove()
}
chart.violinPlots.prepareViolin();
chart.violinPlots.update();
};
chart.violinPlots.reset = function () {
chart.violinPlots.change(defaultOptions)
};
chart.violinPlots.show = function (opts) {
if (opts !== undefined) {
opts.show = true;
if (opts.reset) {
chart.violinPlots.reset()
}
} else {
opts = {show: true};
}
chart.violinPlots.change(opts);
};
chart.violinPlots.hide = function (opts) {
if (opts !== undefined) {
opts.show = false;
if (opts.reset) {
chart.violinPlots.reset()
}
} else {
opts = {show: false};
}
chart.violinPlots.change(opts);
};
/**
* Update the violin obj values
*/
chart.violinPlots.update = function () {
var cName, cViolinPlot;
for (cName in chart.groupObjs) {
cViolinPlot = chart.groupObjs[cName].violin;
// Build the violins sideways, so use the yScale for the xScale and make a new yScale
var xVScale = chart.yScale.copy();
// Create the Kernel Density Estimator Function
cViolinPlot.kde = kernelDensityEstimator(eKernel(vOpts.bandwidth), xVScale.ticks(vOpts.resolution));
cViolinPlot.kdedata = cViolinPlot.kde(chart.groupObjs[cName].values);
var interpolateMax = chart.groupObjs[cName].metrics.max,
interpolateMin = chart.groupObjs[cName].metrics.min;
if (vOpts.clamp == 0 || vOpts.clamp == -1) { //
// When clamp is 0, calculate the min and max that is needed to bring the violin plot to a point
// interpolateMax = the Minimum value greater than the max where y = 0
interpolateMax = d3.min(cViolinPlot.kdedata.filter(function (d) {
return (d.x > chart.groupObjs[cName].metrics.max && d.y == 0)
}), function (d) {
return d.x;
});
// interpolateMin = the Maximum value less than the min where y = 0
interpolateMin = d3.max(cViolinPlot.kdedata.filter(function (d) {
return (d.x < chart.groupObjs[cName].metrics.min && d.y == 0)
}), function (d) {
return d.x;
});
// If clamp is -1 we need to extend the axes so that the violins come to a point
if (vOpts.clamp == -1) {
kdeTester = eKernelTest(eKernel(vOpts.bandwidth), chart.groupObjs[cName].values);
if (!interpolateMax) {
var interMaxY = kdeTester(chart.groupObjs[cName].metrics.max);
var interMaxX = chart.groupObjs[cName].metrics.max;
var count = 25; // Arbitrary limit to make sure we don't get an infinite loop
while (count > 0 && interMaxY != 0) {
interMaxY = kdeTester(interMaxX);
interMaxX += 1;
count -= 1;
}
interpolateMax = interMaxX;
}
if (!interpolateMin) {
var interMinY = kdeTester(chart.groupObjs[cName].metrics.min);
var interMinX = chart.groupObjs[cName].metrics.min;
var count = 25; // Arbitrary limit to make sure we don't get an infinite loop
while (count > 0 && interMinY != 0) {
interMinY = kdeTester(interMinX);
interMinX -= 1;
count -= 1;
}
interpolateMin = interMinX;
}
}
// Check to see if the new values are outside the existing chart range
// If they are assign them to the master _yDomainVP
if (!vOpts._yDomainVP) vOpts._yDomainVP = chart.range.slice(0);
if (interpolateMin && interpolateMin < vOpts._yDomainVP[0]) {
vOpts._yDomainVP[0] = interpolateMin;
}
if (interpolateMax && interpolateMax > vOpts._yDomainVP[1]) {
vOpts._yDomainVP[1] = interpolateMax;
}
}
if (vOpts.showViolinPlot) {
chart.update();
xVScale = chart.yScale.copy();
// Need to recalculate the KDE because the xVScale changed
cViolinPlot.kde = kernelDensityEstimator(eKernel(vOpts.bandwidth), xVScale.ticks(vOpts.resolution));
cViolinPlot.kdedata = cViolinPlot.kde(chart.groupObjs[cName].values);
}
cViolinPlot.kdedata = cViolinPlot.kdedata
.filter(function (d) {
return (!interpolateMin || d.x >= interpolateMin)
})
.filter(function (d) {
return (!interpolateMax || d.x <= interpolateMax)
});
}
for (cName in chart.groupObjs) {
cViolinPlot = chart.groupObjs[cName].violin;
// Get the violin width
var objBounds = getObjWidth(vOpts.width, cName);
var width = (objBounds.right - objBounds.left) / 2;
var yVScale = d3.scale.linear()
.range([width, 0])
.domain([0, d3.max(cViolinPlot.kdedata, function (d) {return d.y;})])
.clamp(true);
var area = d3.svg.area()
.interpolate(vOpts.interpolation)
.x(function (d) {return xVScale(d.x);})
.y0(width)
.y1(function (d) {return yVScale(d.y);});
var line = d3.svg.line()
.interpolate(vOpts.interpolation)
.x(function (d) {return xVScale(d.x);})
.y(function (d) {return yVScale(d.y)});
if (cViolinPlot.objs.left.area) {
cViolinPlot.objs.left.area
.datum(cViolinPlot.kdedata)
.attr("d", area);
cViolinPlot.objs.left.line
.datum(cViolinPlot.kdedata)
.attr("d", line);
cViolinPlot.objs.right.area
.datum(cViolinPlot.kdedata)
.attr("d", area);
cViolinPlot.objs.right.line
.datum(cViolinPlot.kdedata)
.attr("d", line);
}
// Rotate the violins
cViolinPlot.objs.left.g.attr("transform", "rotate(90,0,0) translate(0,-" + objBounds.left + ") scale(1,-1)");
cViolinPlot.objs.right.g.attr("transform", "rotate(90,0,0) translate(0,-" + objBounds.right + ")");
}
};
/**
* Create the svg elements for the violin plot
*/
chart.violinPlots.prepareViolin = function () {
var cName, cViolinPlot;
if (vOpts.colors) {
chart.violinPlots.color = getColorFunct(vOpts.colors);
} else {
chart.violinPlots.color = chart.colorFunct
}
if (vOpts.show == false) {return}
for (cName in chart.groupObjs) {
cViolinPlot = chart.groupObjs[cName].violin;
cViolinPlot.objs.g = chart.groupObjs[cName].g.append("g").attr("class", "violin-plot");
cViolinPlot.objs.left = {area: null, line: null, g: null};
cViolinPlot.objs.right = {area: null, line: null, g: null};
cViolinPlot.objs.left.g = cViolinPlot.objs.g.append("g");
cViolinPlot.objs.right.g = cViolinPlot.objs.g.append("g");
if (vOpts.showViolinPlot !== false) {
//Area
cViolinPlot.objs.left.area = cViolinPlot.objs.left.g.append("path")
.attr("class", "area")
.style("fill", chart.violinPlots.color(cName));
cViolinPlot.objs.right.area = cViolinPlot.objs.right.g.append("path")
.attr("class", "area")
.style("fill", chart.violinPlots.color(cName));
//Lines
cViolinPlot.objs.left.line = cViolinPlot.objs.left.g.append("path")
.attr("class", "line")
.attr("fill", 'none')
.style("stroke", chart.violinPlots.color(cName));
cViolinPlot.objs.right.line = cViolinPlot.objs.right.g.append("path")
.attr("class", "line")
.attr("fill", 'none')
.style("stroke", chart.violinPlots.color(cName));
}
}
};
function kernelDensityEstimator(kernel, x) {
return function (sample) {
return x.map(function (x) {
return {x:x, y:d3.mean(sample, function (v) {return kernel(x - v);})};
});
};
}
function eKernel(scale) {
return function (u) {
return Math.abs(u /= scale) <= 1 ? .75 * (1 - u * u) / scale : 0;
};
}
// Used to find the roots for adjusting violin axis
// Given an array, find the value for a single point, even if it is not in the domain
function eKernelTest(kernel, array) {
return function (testX) {
return d3.mean(array, function (v) {return kernel(testX - v);})
}
}
chart.violinPlots.prepareViolin();
d3.select(window).on('resize.' + chart.selector + '.violinPlot', chart.violinPlots.update);
chart.violinPlots.update();
return chart;
};
/**
* Render a box plot on the current chart
* @param options
* @param [options.show=true] Toggle the whole plot on and off
* @param [options.showBox=true] Show the box part of the box plot
* @param [options.showWhiskers=true] Show the whiskers
* @param [options.showMedian=true] Show the median line
* @param [options.showMean=false] Show the mean line
* @param [options.medianCSize=3] The size of the circle on the median
* @param [options.showOutliers=true] Plot outliers
* @param [options.boxwidth=30] The max percent of the group rangeBand that the box can be
* @param [options.lineWidth=boxWidth] The max percent of the group rangeBand that the line can be
* @param [options.outlierScatter=false] Spread out the outliers so they don't all overlap (in development)
* @param [options.outlierCSize=2] Size of the outliers
* @param [options.colors=chart default] The color mapping for the box plot
* @returns {*} The chart object
*/
chart.renderBoxPlot = function (options) {
chart.boxPlots = {};
// Defaults
var defaultOptions = {
show: true,
showBox: true,
showWhiskers: true,
showMedian: true,
showMean: false,
medianCSize: 3.5,
showOutliers: true,
boxWidth: 30,
lineWidth: null,
scatterOutliers: false,
outlierCSize: 2.5,
colors: chart.colorFunct,
padding: 0
};
chart.boxPlots.options = shallowCopy(defaultOptions);
for (var option in options) {
chart.boxPlots.options[option] = options[option]
}
var bOpts = chart.boxPlots.options;
//Create box plot objects
for (var cName in chart.groupObjs) {
chart.groupObjs[cName].boxPlot = {};
chart.groupObjs[cName].boxPlot.objs = {};
}
/**
* Calculates all the outlier points for each group
*/
!function calcAllOutliers() {
/**
* Create lists of the outliers for each content group
* @param cGroup The object to modify
* @return null Modifies the object in place
*/
function calcOutliers(cGroup) {
var cExtremes = [];
var cOutliers = [];
var cOut, idx;
for (idx = 0; idx <= cGroup.values.length; idx++) {
cOut = {value: cGroup.values[idx]};
if (cOut.value < cGroup.metrics.lowerInnerFence) {
if (cOut.value < cGroup.metrics.lowerOuterFence) {
cExtremes.push(cOut);
} else {
cOutliers.push(cOut);
}
} else if (cOut.value > cGroup.metrics.upperInnerFence) {
if (cOut.value > cGroup.metrics.upperOuterFence) {
cExtremes.push(cOut);
} else {
cOutliers.push(cOut);
}
}
}
cGroup.boxPlot.objs.outliers = cOutliers;
cGroup.boxPlot.objs.extremes = cExtremes;
}