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<!DOCTYPE html>
<html>
<title>
Genetic Drift Visualisation Tool
</title>
<!-- CSS and JS Libraries (Start) -->
<head>
<link rel='stylesheet' type='text/css' href='css/toolStyle.css'>
<script src='libraries/jquery-3.1.1.min.js'></script>
<script src='libraries/math.min.js'></script>
<script src='libraries/Timer.js'></script>
<script type='text/javascript' src='https://www.gstatic.com/charts/loader.js'></script>
<script type='text/javascript'>
google.charts.load('current', {packages: ['corechart', 'bar', 'line', 'controls']});
</script>
</head>
<!-- CSS and JS Libraries (End) -->
<body>
<!-- Top Matter HTML (Start) -->
<div class='main' id='header'>
Genetic Drift Visualisation Tool
</div>
<ul class='toolbar'>
<li class='current' data-tab='jsBody_Output' id='dummy_Output'>Output</li>
<li data-tab='jsBody_Parameters'>Parameters</li>
<li data-tab='jsBody_About'>About</li>
</ul>
<!-- Top Matter HTML (End) -->
<!-- Output Tab HTML (Start) -->
<div class='main toolbar-content current' id='jsBody_Output'>
<div id='output_heading'>
<ul class='output_headingList'>
<li>
<span id='output_headingChild'>
Generation: <span id='output_genNum'></span>
</span>
<span class='paraMag_space'></span>
<span id='output_headingChildToo'>
F<sub>ST</sub>: <span id='output_fst'></span>
</span>
</li>
<li>
<span class='paraMag_space'></span>
Simulate next <i>n</i> generations:
<button class='output_simButton' howMany='1'>n = 1 </button>
<button class='output_simButton' howMany='10'>n = 10</button>
<button class='output_simButton' howMany='output_simInput'>n =</button>
<input id='output_simInput' type='number' min=1 max=1000>
<span class='paraMag_space'></span>
<button id='output_interrupt' disabled='true'>Stop</button>
<span class='paraMag_space'></span>
<button id='output_reset'>Reset</button>
</li>
<li>
<div id="output_progressBarContainer">
<div id="output_progressBar">
<div id="output_progressNumber">
<span id="output_progressNumberChild">0</span>%
</div>
</div>
</div>
</li>
</ul>
</div>
<div id='jsBody_Container'>
<div id='output_L'>
<ul class='output_ulL'>
<li class='current' data-tab='output_alleleFreqChart'>Allele Frequencies</li>
<li data-tab='output_indivAlleleContainer'>Individual Alleles</li>
</ul>
<div class='output_chartContainer'>
<div class='output_chartDim current' id='output_alleleFreqChart'></div>
<div class='output_chartDim' id='output_indivAlleleContainer'>
<canvas class='output_indivAlleleChart' id='output_iacForeground'></canvas>
<canvas class='output_indivAlleleChart' id='output_iacMidground'></canvas>
<canvas class='output_indivAlleleChart' id='output_iacBackground'></canvas>
</div>
</div>
</div>
<div id='output_R'>
<ul class='output_ulR'>
<li class='current' data-tab='output_fstDashboard'>Conancestry Coefficient</li>
<li data-tab='output_alleleFreqChartToo'>Allele Frequencies</li>
</ul>
<div class='output_chartContainerToo'>
<div class='output_chartDimToo current' id='output_fstDashboard'>
<div id='output_fstChart'></div>
<div id='output_fstControl'></div>
</div>
<div class='output_chartDimToo' id='output_alleleFreqChartToo'>
</div>
</div>
</div>
</div>
<div id='output_curParaMagContainer'>
Current Parameters:
<ul class='output_curParaMag'>
<li>Number of Populations: <span id='output_numOfPop'></span></li>
<li>Population Size: <span id='output_popSize'></span></li>
<li>Number of Allele Types: <span id='output_numOfAlleles'></span></li>
<li>Mutation Denominator: <span id='output_mutaDenom'></span></li>
<li>Number of Migrants: <span id='output_numOfMigrants'></span></li>
<li>Initial Number of Simulations: <span id='output_init'></span></li>
<li>Simulation Rate: <span id='output_simRate'></span></li>
</ul>
</div>
</div>
<!-- Output Tab HTML (End) -->
<!-- Parameters Tab HTML (Start) -->
<div class='main toolbar-content' id='jsBody_Parameters'>
<div id='jsBody_Container'>
<ul class='paraMag' id='paraMag_L'>
<li>
Number of Populations: <input id='paraMag_numOfPop' type='number' min=1 max=10> <br>
<span class='paraMag_Info'>
Sets the number of populations to observe in the simulation routine. <br> Takes an integer value between 1 and 10 (inclusive).
</span>
</li>
<li>
Population Size: <input id='paraMag_popSize' type='number' min=50 max=500> <br>
<span class='paraMag_Info'>
Sets a population's <b>fixed</b> size in the simulation routine. Takes an integer value between 50 and 500 (inclusive).
</span>
</li>
<li>
Number of Allele Types: <input id='paraMag_numOfAlleles' type='number' min=2 max=8> <br>
<span class='paraMag_Info'>
Sets and limits the number of possible allele types in a population. Takes an integer value between 2 and 8 (inclusive).
</span>
</li>
<li>
Mutation Denominator: <input id='paraMag_mutaDenom' type='number' min=0 max=1000> <br>
<span class='paraMag_space'></span><input class='paraMag_slider' id='paraMag_mutaDenomChild' type='range' min=0 max=1000 step=1> <br>
<span class='paraMag_Info'>
Sets the denominator of an allele's mutation rate. An allele currently has <br> <span id='paraMag_mutaDenomChildToo'></span> chance to mutate into a different allele type. Takes an integer <br> value between 1 and 1000 (inclusive).
</span>
</li>
<li>
Number of Migrants: <input id='paraMag_numOfMigrants' type='number' min=0 max=499> <br>
<span class='paraMag_Info'>
Sets the number of members who migrate each generation. Takes an integer value between 0 and <span id='paraMag_numOfMigrantsChild'></span> (inclusive).
</span>
</li>
<li>
Initial Number of Simulations: <input id='paraMag_init' type='number' min=1 max=1000> <br>
<span class='paraMag_Info'>
Sets the number of simulations to conduct before the user can interact with the <b>Output</b> page. Takes an integer value between 1 and 1000 (inclusive).
</span>
</li>
<li>
Simulation Rate: <input id='paraMag_simRate' type='number' min=0.01 max=2 step=0.01> <br>
<span class='paraMag_space'></span><input id='paraMag_simRateChild' type='range' min=0.01 max=2 step=0.01> <br>
<span class='paraMag_Info'>
Sets the timer rate of executing consecutive simulations. The user interruption button will be more responsive if the Simulation Rate is set to a high value. Takes a value between 0.01 and 2.00 seconds (inclusive).
</span>
</li>
</ul>
<ul class='paraMag' id='paraMag_R'>
<li>
<button id='paraMag_submit'>Submit Parameters</button> <br>
</li>
<li id='small'>
<input id='paraMag_show' type='checkbox'>Show detailed information
</li>
</ul>
</div>
</div>
<!-- Parameters Tab HTML (Start) -->
<!-- About Tab HTML (Start) -->
<div class='main toolbar-content' id='jsBody_About'>
F<sub>ST</sub> is a useful statistic for summarising the observed genetic drift for a group of populations (Weir, 1996). F<sub>ST</sub>
is defi ned to be a value between 0 and 1 (inclusive). A small value of F<sub>ST</sub> proposes that the individuals
in the same subpopulation are not very related to each other. A high value of F<sub>ST</sub> suggests that individuals in the same
subpopulation are quite related to each other. We estimate F<sub>ST</sub> using an analysis of variance framework. Hence, F<sub>ST</sub>
can produce a negative estimate, which is out of the bounds of because an unbiased estimator is used to estimate F<sub>ST</sub>. But,
the size of the bias is quite minute, and F<sub>ST</sub> is only imprecise when the true F<sub>ST</sub> is exceptionally close to zero.
There is also a case when F<sub>ST</sub> is a ratio of zeroes. The phenomenon occurs when the same allele is present in all populations.
Hence, for this particular event, F<sub>ST</sub> is defined to be equal to one because the observed populations are in fact inbred,
just not in the expected fashion.
<br>
<br>
<span id='small'>
Weir, B. S. (1996). Genetic data analysis II. methods for discrete population genetic
data. Sinauer Associates, Inc. Publishers.
</span>
<hr>
The mutation scheme used was based on the stepwise mutation model proposed
by Kimura & Ohta (1978), with a minor modi cation to respect the
boundaries. For example, there are ve possible alleles in a population, Alleles
A, B, C, D, and E. Allele B can mutate to either Allele A or Allele C,
and a similar process applies to Allele D, and Allele E. However, Allele A and
Allele E can only mutate to Allele B and Allele D, respectively.
<br>
<br>
<span id='small'>
Kimura, M., & Ohta, T. (1978). Stepwise mutation model and distribution of
allelic frequencies in a finite population. Proceedings of the National Academy of
Sciences, 75(6), 2868–2872.
</span>
<hr>
The migration scheme used simple random sampling to select a xed number
of migrants from each of the populations. These migrants then immigrated
to a randomly chosen population, excluding their population of origin. As a
result, populations before breeding were not necessarily the speci ed population
size. However, this simple scheme was computationally quick to execute
as there are no constraints to enforce. Since the end users are typically going
to be students, implementing a more complex migration scheme that might
signi cantly increase the simulation time could frustrate the end user.
<hr>
Libraries and resources used for this web application include:
<ul>
<li>ColorBrewer from <a href='http://colorbrewer2.org/'>colorbrewer2.org/</a>.</li>
<li>Google Charts API from <a href='https://developers.google.com/chart/'>developers.google.com/chart/</a>.</li>
<li>jQuery from <a href='https://jquery.com'>jquery.com</a>.</li>
<li>Math.js from <a href='http://mathjs.org'>mathjs.org</a>.</li>
<li>Timer.js from <a href='https://github.com/fschaefer/Timer.js'>github.com/fschaefer/Timer.js</a>.</li>
</ul>
</div>
<!-- About Tab HTML (End) -->
<!-- Bottom Matter HTML (Start) -->
<div class='main' id='copyright'>
Genetic Drift Visualisation Tool ver 0.3.0 <br>
© 2016-2017 David Chan
</div>
<!-- Bottom Matter HTML (End) -->
<!-- Initialisation of JS Functionality (Start) -->
<script src='scripts/main.js'></script>
<script src='scripts/parameters.js'></script>
<script src='scripts/output.js'></script>
<script src='scripts/indivAllele.js'></script>
<script>
var parameters = {
// Parameters Tab.
numOfPop: 5, // Number of Populations.
popSize: 50, // Population Size.
numOfAlleles: 8, // Number of Allele Types.
mutationDenom: 300, // Mutation Denom.
numOfMigrants: 0, // Number of Migrants.
init: 1, // Initial Number of Simulations.
simRate: 10, // Simulation Rate.
// Output Tab.
simInput: 100 // Number of simulations to do consecutively.
},
alleles = new allelePool(), // Stores the allelePool object and it's methods.
rngBin = new randomBinary(), // Stores the binary random number generator object.
allSpecies = [], // Stores the simulation routine.
webpageLive = false, // Tracks whether the webpage has been loaded already.
timerVars = {
// Stores the timer variables to get Javascript thinking in more than one thread.
toGenNum: 0, // Tracks how many generations to process for the
// simulation routine.
toStop: false, // Tracks whether the user has interrupted the simulation
// routine.
tickTock: new Timer(10), // The timer object.
increment: 0, // How much to increment the progress bar by.
progress: 0, // Current state of the progress bar.
progressMax: parseInt( // Parse the CSS field for how wide the progress bar is.
$('#output_progressBarContainer').css('width'), 10
)
},
scope = {
// Object variable to hold constants for fstCalc().
//ni: n_i,
//twoNi: 2*n_i,
//nBar: (n_1 + n_2 + . . . + n_r)/r,
//a: nBar - 1,
//b: (r - 1)/1,
//c: rp*(nBar - 1),
//d: r*(nBar - nC)/nBar,
//e: (nBar - 1) + (r - 1)*(nBar - nC),
//f: (nBar - nC)/(4*nC^2)
//g: n_1 + n_2 + . . . + n_r,
//h: (r - 1)*nBar
// Where r: parameters.numOfPop,
// and nC: (n_1 + . . . + n_r - [n_1^2 + . . . + n_r^2]/[n_1 + . . . + n_r])/(r - 1).
},
alleleFreq = {
// Chart options for visualising the allele frequencies.
options: {
title: 'Allele Frequencies (Parent Generation)',
height: 500,
width: 600,
bar: {
groupWidth: '70%'
},
hAxis: {
title: 'Population'
},
vAxis: {
title: 'Allele Frequency (%)',
minValue: 0,
maxValue: 1
},
isStacked: 'percent',
animation: {
duration: 1000, // in milliseconds
easing: 'out'
},
tooltip: {
isHtml: true
}
}
//data: new google.visualization.DataTable(), // Stores the allele frequencies.
//chart: new google.visualization.ColumnChart(), // The chart object.
//view: new google.visualization.DataView() // The view of the datatable object to
// visualise.
},
fst = {
// Chart options for visualising the conancestry coefficient.
optionsChart: {
title: 'Coancestry Coefficient over Generations',
height: 450,
width: 500,
hAxis: {
title: 'Generation',
minValue: 1,
gridlines: {
count: 5
}
},
vAxis: {
title: 'Coancestry Coefficient (FST)',
viewWindowMode: 'pretty',
},
legend: {
position: 'none'
},
animation: {
duration: 1000, // in milliseconds
easing: 'out'
},
tooltip: {
isHtml: true
}
},
optionsControl: {
filterColumnIndex: 0,
ui: {
chartOptions: {
height: 50,
width: 500
},
snapToData: true
}
}
//data: new google.visualization.DataTable(), // Stores the conancestry coefficient.
//chart: new google.visualization.ChartWrapper(), // The chart object.
//view: new google.visualization.DataView(), // The view of the datatable object to
// visualise.
//control: google.visualization.ControlWrapper(), // The controls object.
//dashboard: new google.visualization.Dashboard() // The dashboard instance which stores
// the chart and control objects.
},
indivAllele = {
options: {
title: 'Individual Alleles (Parent Generation)',
backgroundColor: 'white',
height: 500,
width: 600
},
tickTock: new Timer(100)
//data: new google.visualization.DataTable(), // The data table object.
//chart: new indivAlleleChart(background, midground, foreground) // The chart object which is made
// up of three <canvas>s.
},
alleleFreqChild = {
// Chart options for visualising the allele frequencies.
options: {
title: 'Allele Frequencies (Child Generation)',
height: 500,
width: 500,
bar: {
groupWidth: '70%'
},
hAxis: {
title: 'Population'
},
vAxis: {
title: 'Allele Frequency (%)',
minValue: 0,
maxValue: 1
},
isStacked: 'percent',
animation: {
duration: 1000, // in milliseconds
easing: 'out'
},
tooltip: {
isHtml: true
}
}
//data: new google.visualization.DataTable(), // Stores the allele frequencies.
//chart: new google.visualization.ColumnChart(), // The chart object.
//view: new google.visualization.DataView() // The view of the datatable object to
// visualise.
};
paraMag_submit.prop('disabled', true);
output_reset.prop('disabled', true);
output_simButtons.prop('disabled', true);
output_genNum.html('. . .');
output_fst.html('. . .');
parameters_Initialise();
google.charts.setOnLoadCallback(output_Initialise);
</script>
<!-- Initialisation of JS Functionality (End) -->
</body>
</html>