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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<title>
Qurro
</title>
<link rel="shortcut icon" href="icon.png" />
<link rel="stylesheet" href="vendor/bootstrap.min.css" />
<link rel="stylesheet" href="qurro.css" />
<link rel="stylesheet" href="vendor/dataTables.bootstrap4.min.css" />
</head>
<body>
<div class="centeredBlock mt-3" id="loadingMessage">
<strong>
Loading Qurro plots; this might take a few seconds...
</strong>
</div>
<div class="twoColumnRow">
<div id="topLeftDiv">
<div id="rankPlot"></div>
<!-- input group structure based on Bootstrap docs:
https://getbootstrap.com/docs/4.3/components/input-group/#custom-select
-->
<div class="input-group input-group-sm mb-1">
<div class="input-group-prepend">
<label class="input-group-text" for="rankField">
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This dropdown changes the feature ranking used in the rank plot. Changing this will adjust each feature's y-axis value to match its value for the selected field, and will re-rank the features in ascending order in the rank plot."
>
</span>
<!-- will be filled with either "Differential" or
"Feature Loading", depending on the input
ranking type
-->
<span id="rankFieldLabel"></span>
</label>
</div>
<select id="rankField" class="custom-select"> </select>
</div>
<div class="input-group input-group-sm mb-1">
<div class="input-group-prepend">
<label
class="input-group-text"
for="rankPlotColorScheme"
>
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This dropdown changes the colors of selected features in the rank plot."
>
</span>
Color scheme
</label>
</div>
<select id="rankPlotColorScheme" class="custom-select">
<!-- Just normal web colors, with the exception of
"Purple" (which is a bit lighter than the "Purple"
web color).
See https://en.wikipedia.org/wiki/Web_colors.
-->
<option value="#f00,#00f,#949"
>Red, Blue, Purple</option
>
<!-- These colors were taken directly from Figure 3a in
the Songbird paper (Morton/Marotz et al. 2019).
-->
<option value="#5fa2c8,#daa520,#029e73"
>Blue, Gold, Green (Songbird paper)</option
>
<!-- Just normal web colors. -->
<option value="#ff0,#f00,#ff8c00"
>Yellow, Red, Orange</option
>
</select>
</div>
<div class="input-group input-group-sm mb-1">
<!-- HACK: Invisibly fill space: this lets us center the
inputs in this group (by default they're left-aligned)
-->
<input
type="text"
disabled
class="form-control hackySpacerInput"
/>
<div class="input-group-prepend">
<label class="input-group-text" for="barSizeSlider">
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title='This slider adjusts the width of each bar in the rank plot. In order for this slider to take effect, the "fit bar widths" checkbox must be unchecked.'
>
</span>
Bar width
</label>
<div class="input-group-text">
<input
id="barSizeSlider"
type="range"
min="1"
max="10"
value="1"
/>
</div>
</div>
<div class="input-group-append">
<label
class="input-group-text"
for="fitBarSizeCheckbox"
>
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="When checked, this scales the widths of bars in the rank plot so that the rank plot takes up a constant width (ignoring what the bar width slider is set to). This is useful for displaying rank plots with either a ton of features or a tiny amount of features."
>
</span>
Fit bar widths to a constant plot width?
</label>
<div class="input-group-text">
<input type="checkbox" id="fitBarSizeCheckbox" />
</div>
</div>
<input
type="text"
disabled
class="form-control hackySpacerInput"
/>
</div>
<div class="input-group input-group-sm mb-1">
<input
type="text"
disabled
class="form-control hackySpacerInput"
/>
<div class="input-group-prepend">
<label class="input-group-text">
<span
class="questionmark mr-0"
data-toggle="tooltip"
data-placement="top"
title="This button exports a TSV file listing just the selected numerator and/or denominator features (in no particular order). Below the header row in the TSV file, each row contains a feature ID and its log-ratio classification."
>
</span>
</label>
<button
id="exportRankPlotDataButton"
class="btn btn-outline-secondary btn-sm"
>
Export currently selected features
</button>
</div>
<input
type="text"
disabled
class="form-control hackySpacerInput"
/>
</div>
<p
id="barSizeWarning"
class="alert alert-warning centeredBlock invisible mt-3 mb-3"
>
<strong>Warning:</strong> The rank plot is currently using a
bar width of less than one pixel per bar. This means that
the image shown isn't necessarily going to be an accurate
representation of the rank plot.
</p>
</div>
<div id="topRightDiv">
<div id="samplePlot"></div>
<div class="centeredBlock">
<!-- NOTE that the scale/field select values below will be
literally used in the JSON.
Also, the first-listed one is the default. Since the
default x-axis is the balance (quant.) and the default
color is the sample ID (nom.), we adjust the default
scale types accordingly.
-->
<div class="input-group input-group-sm mb-1">
<div class="input-group-prepend">
<label class="input-group-text" for="xAxisField">
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This dropdown changes the sample metadata field used for the sample plot's x-axis."
>
</span>
x-axis field
</label>
</div>
<select class="custom-select" id="xAxisField"> </select>
<div class="input-group-prepend">
<label class="input-group-text" for="xAxisScale">
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This dropdown changes the scale type of the sample plot's x-axis. If the sample metadata field you have selected for 'x-axis field' right now is numeric (e.g. participant weight), you probably want a quantitative scale type; if it's ordinal or nominal (e.g. subject ID, sample body site), you probably want a categorical scale type."
>
</span>
x-axis scale type
</label>
</div>
<select class="custom-select" id="xAxisScale">
<option value="nominal">Categorical</option>
<option value="quantitative">Quantitative</option>
</select>
</div>
<div class="input-group input-group-sm mb-1">
<div class="input-group-prepend">
<label
class="input-group-text"
id="colorFieldLabel"
for="colorField"
>
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This dropdown changes the sample metadata field used to color points in the sample plot."
>
</span>
Color field
</label>
</div>
<select class="custom-select" id="colorField"> </select>
<div class="input-group-prepend">
<label
class="input-group-text"
id="colorScaleLabel"
for="colorScale"
>
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This dropdown changes the scale type of the sample coloring used in the sample plot. If the sample metadata field you have selected for 'Color field' right now is numeric (e.g. participant weight), you probably want a quantitative scale type; if it's ordinal or nominal (e.g. subject ID, sample body site), you probably want a categorical scale type."
>
</span>
Color scale type
</label>
</div>
<select class="custom-select" id="colorScale">
<option value="nominal">Categorical</option>
<option value="quantitative">Quantitative</option>
</select>
</div>
<div class="input-group input-group-sm mb-1">
<div class="input-group-prepend">
<label
class="input-group-text"
id="catColorSchemeLabel"
for="catColorScheme"
>
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This dropdown changes the color scheme used for categorical color scales in the sample plot."
>
</span>
Categorical color scheme
</label>
</div>
<select class="custom-select" id="catColorScheme">
<option value="accent">accent</option>
<option value="category10">category10</option>
<option value="category20">category20</option>
<option value="category20b">category20b</option>
<option value="category20c">category20c</option>
<option value="qiimediscrete"
>Classic QIIME Colors</option
>
<option value="dark2">dark2</option>
<option value="paired">paired</option>
<option value="pastel1">pastel1</option>
<option value="pastel2">pastel2</option>
<option value="set1">set1</option>
<option value="set2">set2</option>
<option value="set3">set3</option>
<option value="tableau10" selected="true"
>tableau10</option
>
<option value="tableau20">tableau20</option>
</select>
<div class="input-group-prepend">
<label
class="input-group-text"
id="quantColorSchemeLabel"
for="quantColorScheme"
>
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This dropdown changes the color scheme used for quantitative color scales in the sample plot."
>
</span>
Quantitative color scheme
</label>
</div>
<select class="custom-select" id="quantColorScheme">
<optgroup label="Sequential Single-Hue">
<option value="blues" selected="true"
>blues</option
>
<option value="tealblues">tealblues</option>
<option value="teals">teals</option>
<option value="greens">greens</option>
<option value="browns">browns</option>
<option value="oranges">oranges</option>
<option value="reds">reds</option>
<option value="purples">purples</option>
<option value="warmgreys">warmgreys</option>
<option value="greys">greys</option>
</optgroup>
<optgroup label="Sequential Multi-Hue">
<option value="viridis">viridis</option>
<option value="magma">magma</option>
<option value="inferno">inferno</option>
<option value="plasma">plasma</option>
<option value="bluegreen">bluegreen</option>
<option value="bluepurple">bluepurple</option>
<option value="goldgreen">goldgreen</option>
<option value="goldorange">goldorange</option>
<option value="goldred">goldred</option>
<option value="greenblue">greenblue</option>
<option value="orangered">orangered</option>
<option value="purplebluegreen"
>purplebluegreen</option
>
<option value="purpleblue">purpleblue</option>
<option value="purplered">purplered</option>
<option value="redpurple">redpurple</option>
<option value="yellowgreenblue"
>yellowgreenblue</option
>
<option value="yellowgreen">yellowgreen</option>
<option value="yelloworangebrown"
>yelloworangebrown</option
>
<option value="yelloworangered"
>yelloworangered</option
>
<option value="darkblue">darkblue</option>
<option value="darkgold">darkgold</option>
<option value="darkgreen">darkgreen</option>
<option value="darkmulti">darkmulti</option>
<option value="darkred">darkred</option>
<option value="lightgreyred"
>lightgreyred</option
>
<option value="lightgreyteal"
>lightgreyteal</option
>
<option value="lightmulti">lightmulti</option>
<option value="lightorange">lightorange</option>
<option value="lighttealblue"
>lighttealblue</option
>
</optgroup>
<optgroup label="Diverging">
<option value="blueorange">blueorange</option>
<option value="brownbluegreen"
>brownbluegreen</option
>
<option value="purplegreen">purplegreen</option>
<option value="pinkyellowgreen"
>pinkyellowgreen</option
>
<option value="purpleorange"
>purpleorange</option
>
<option value="redblue">redblue</option>
<option value="redgrey">redgrey</option>
<option value="redyellowblue"
>redyellowblue</option
>
<option value="redyellowgreen"
>redyellowgreen</option
>
<option value="spectral">spectral</option>
</optgroup>
<optgroup label="Cyclical">
<option value="rainbow">rainbow</option>
<option value="sinebow">sinebow</option>
</optgroup>
</select>
</div>
<div class="input-group input-group-sm mb-1">
<input
type="text"
disabled
class="form-control hackySpacerInput"
/>
<div class="input-group-prepend">
<label
class="input-group-text"
for="boxplotCheckbox"
>
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="When checked, the sample plot will display a boxplot (rather than a scatterplot) whenever the x-axis scale type is categorical."
>
</span>
Use boxplots for categorical data?
</label>
<div class="input-group-text">
<input type="checkbox" id="boxplotCheckbox" />
</div>
</div>
<div class="input-group-prepend">
<label
class="input-group-text"
for="borderCheckbox"
>
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="When checked, all samples in the sample plot will have black borders drawn around them. This can be useful if the selected color scheme includes colors that are hard to see on a white background. Will only take effect when the sample plot is a scatterplot, not a boxplot."
>
</span>
Draw borders on scatterplot points?
</label>
<div class="input-group-text">
<input type="checkbox" id="borderCheckbox" />
</div>
</div>
<input
type="text"
disabled
class="form-control hackySpacerInput"
/>
</div>
<div class="input-group input-group-sm mb-1">
<input
type="text"
disabled
class="form-control hackySpacerInput"
/>
<div class="input-group-prepend">
<label class="input-group-text">
<span
class="questionmark mr-0"
data-toggle="tooltip"
data-placement="top"
title="This button exports a TSV file describing the data underlying the sample plot. Below the header row in the TSV file, each row contains a sample's ID along with the sample's currently selected log-ratio and its metadata values for the current x-axis and color fields."
>
</span>
</label>
<button
id="exportSamplePlotDataButton"
class="btn btn-outline-secondary btn-sm"
>
Export current sample plot data
</button>
</div>
<input
type="text"
disabled
class="form-control hackySpacerInput"
/>
</div>
<div
id="mainSamplesDroppedDiv"
class="centeredBlock sampleRemovedDiv invisible"
></div>
<div
id="balanceSamplesDroppedDiv"
class="centeredBlock sampleRemovedDiv invisible"
></div>
<div
id="xAxisSamplesDroppedDiv"
class="centeredBlock sampleRemovedDiv invisible"
></div>
<div
id="colorSamplesDroppedDiv"
class="centeredBlock sampleRemovedDiv invisible"
></div>
</div>
</div>
</div>
<div class="twoColumnRow">
<div id="botLeftDiv">
<p
id="commonFeatureWarning"
class="alert alert-warning centeredBlock invisible mt-3 mb-2"
>
<strong>Warning:</strong> Currently, ___ feature(s) are
selected in both the numerator and denominator of the
log-ratio. We strongly suggest you instead look at a
log-ratio that doesn't contain common features in the
numerator and denominator.
</p>
<!-- Note for future reference: whitespace between the
start and end tag of a textarea is apparently
interpreted as just that, and preserved in the textarea
on the page.
(So that's why the textarea declarations below are on
long lines.)
-->
<div class="centeredBlock">
<h4 id="numHeader" class="centeredHeader">
Numerator Features
</h4>
<!-- Same table classes as in
https://datatables.net/examples/styling/bootstrap4.html
used, but with table-sm added.
-->
<table
id="topFeaturesDisplay"
class="table table-striped table-bordered table-sm"
></table>
</div>
<div id="divide" class="centeredBlock"></div>
<div class="centeredBlock">
<h4 id="denHeader" class="centeredHeader">
Denominator Features
</h4>
<table
id="botFeaturesDisplay"
class="table table-striped table-bordered table-sm"
></table>
</div>
</div>
<div id="botRightDiv">
<h4 class="centeredHeader">Autoselecting Features</h4>
<div class="input-group input-group-sm">
<div class="input-group-prepend">
<label class="input-group-text" for="autoSelectNumber">
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This group of controls supports autoselection, which is a quick way of taking the log-ratio of the highest- to the lowest- ranked features in the rank plot. The text box in the middle here specifies the number of features (or the percentage of features) to select from each side of the rank plot for a log-ratio. You can put down a negative number to flip the selection (selecting the log-ratio of the lowest- to highest-ranked features). Ties are broken arbitrarily."
>
</span>
Using the current ranking, select the top and bottom
</label>
</div>
<input
type="number"
class="form-control"
id="autoSelectNumber"
step="any"
/>
<select class="custom-select" id="autoSelectType">
<option value="autoPercent">% of features</option>
<option value="autoLiteral">features</option>
</select>
<!-- Based on
https://getbootstrap.com/docs/4.0/components/input-group/#button-addons
-->
<div class="input-group-append">
<button
class="btn btn-outline-secondary"
id="autoSelectButton"
>
Apply
</button>
</div>
</div>
<h4 class="centeredHeader mt-2">
Selecting Features by Filtering
</h4>
<div class="input-group input-group-sm">
<div class="input-group-prepend">
<label class="input-group-text" for="topSearch">
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This group of controls supports using various filtering methods to select features for the numerator of a log-ratio. To perform selection using these filtering controls, press the 'Apply Filtering' button below."
>
</span>
Filter numerator to features where
</label>
</div>
<select class="custom-select num" id="topSearch"> </select>
<div class="input-group-prepend">
<label class="input-group-text">
<span
class="questionmark mr-0"
data-toggle="tooltip"
data-placement="top"
title="The next selector adjusts the method used to filter features by a feature metadata / ranking field. Most of these methods should be self-explanatory; please see the Selection Tutorial (linked from Qurro's README) for information on the details of these methods, and some examples of using them."
>
</span>
</label>
</div>
<select class="custom-select num" id="topSearchType">
<optgroup label="Text searching (case insensitive)">
<option value="text">contains the text</option>
<option value="or"
>contains text separated by | (pipe)</option
>
<option value="nottext"
>is provided, and does not contain the
text</option
>
<option value="rank"
>contains the separated text fragment(s)</option
>
</optgroup>
<optgroup label="Numeric searching (basic)">
<option value="lt">is less than</option>
<option value="gt">is greater than</option>
<option value="lte"
>is less than or equal to</option
>
<option value="gte"
>is greater than or equal to</option
>
</optgroup>
<!--
<optgroup label="Numeric searching (percentile)">
<option value="topp"
>is in this top percent of values</option
>
<option value="botp"
>is in this bottom percent of values</option
>
</optgroup>
-->
</select>
</div>
<input type="text" class="form-control num" id="topText" />
<div class="input-group input-group-sm mt-2">
<div class="input-group-prepend">
<label class="input-group-text" for="botSearch">
<span
class="questionmark"
data-toggle="tooltip"
data-placement="top"
title="This group of controls supports using various filtering methods to select features for the denominator of a log-ratio. To perform selection using these filtering controls, press the 'Apply Filtering' button below."
>
</span>
Filter denominator to features where
</label>
</div>
<select class="custom-select den" id="botSearch"> </select>
<div class="input-group-prepend">
<label class="input-group-text">
<span
class="questionmark mr-0"
data-toggle="tooltip"
data-placement="top"
title="The next selector adjusts the method used to filter features by a feature metadata / ranking field. Most of these methods should be self-explanatory; please see the Selection Tutorial (linked from Qurro's README) for information on the details of these methods, and some examples of using them."
>
</span>
</label>
</div>
<select class="custom-select den" id="botSearchType">
<optgroup label="Text searching (case insensitive)">
<option value="text">contains the text</option>
<option value="or"
>contains text separated by | (pipe)</option
>
<option value="nottext"
>is provided, and does not contain the
text</option
>
<option value="rank"
>contains the separated text fragment(s)</option
>
</optgroup>
<optgroup label="Numeric searching (basic)">
<option value="lt">is less than</option>
<option value="gt">is greater than</option>
<option value="lte"
>is less than or equal to</option
>
<option value="gte"
>is greater than or equal to</option
>
</optgroup>
<!--
<optgroup label="Numeric searching (percentile)">
<option value="topp"
>is in this top percent of values</option
>
<option value="botp"
>is in this bottom percent of values</option
>
</optgroup>
-->
</select>
</div>
<input type="text" class="form-control den" id="botText" />
<!-- Invisible <a> used for downloading data URIs.
Based on #downloadHelper in MetagenomeScope's viewer
interface.
-->
<a id="downloadHelper" class="invisible"></a>
<div class="input-group input-group-sm mt-3">
<input
type="text"
disabled
class="form-control hackySpacerInput"
/>
<div class="input-group-prepend">
<label class="input-group-text">
<span
class="questionmark mr-0"
data-toggle="tooltip"
data-placement="top"
title="Attempts to select features in a log-ratio based on the filtering controls defined above. Filtering is useful for more focused investigations than in autoselection: for example, imagine filtering to all OTUs classified in a given genus."
>
</span>
</label>
<button
id="multiFeatureButton"
class="btn btn-outline-secondary btn-sm"
>
Apply Filtering
</button>
</div>
<input
type="text"
disabled
class="form-control hackySpacerInput"
/>
</div>
</div>
</div>
<!--
<p>
<label for="selectMicrobesFileSelector">
<strong>
Upload "Select Features" List:
</strong>
</label>
TODO make RRVDisplay get this input by ID
and set its onchange to the RRVDisplay instance's
particular select microbes or whatever function
<input type="file" id="selectMicrobesFileSelector"
onChange="ssmv.uploadSelectMicrobesFile();" />
</p>
<p>
<label for="zeroFillInput">
<strong>
Value to fill in for zero-abundance features:
</strong>
</label>
<input type="number" id="zeroFillInput" min="0"
max="1000" value="0">
</input>
</p>
-->
<!-- This file will be edited by the Qurro python script to
contain definitions for the rank plot and sample plot JSON,
and will use these to create an instance of RRVDisplay
(thereby starting Qurro).
Leaving this code at the bottom of the page is sufficient to wait
until the rest of the stuff in the page has been loaded:
see https://stackoverflow.com/a/1861233.
We need to wait for the page to load before calling
RRVDisplay.makePlots(); otherwise, we'll get (at least) the error
"ERROR: Signal bind element not found: null" described at
https://github.com/vega/vega-embed/issues/64.
-->
<script data-main="main" src="vendor/require.js"></script>
</body>
</html>