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README.md

Pandemix

Overview

Pandemix gives the ability to quickly create interactive web pages based on phylogenetic virus data. The library contains a number of panels that can be told to render in a specified spot on a page with a few lines of code. The panels themselves can be styled through CSS to fit into the design of your website. The Pandemix panels are interactive and linked. For example, selecting some nodes in a tree type panel will select the same nodes in all other tree panels and highlight the geographical locations associated with the nodes on the map. Selecting a date on the time line panel will highlight the same date in tree panels and display the geographical distribution of reported viral cases at the selected time. These features allow you to quickly set up a rich sharing and data exploration web page for emerging viruses.

Installation

Download Pandemix
To use Pandemix in your web page, you need to include it in your HTML. If all you need is Pandemix, include pandemix-min.js, pandemix.css and sprites.png in your HTML. However, Pandemix depends on D3 and Crossfilter for most things and Leaflet for maps, so you should include a copy of those as well.
allMin.js includes pandemix-min as well as a version of the 3 other librariers it depends on.

Usage pattern

You must first create a div somewhere on your page and give it an id. This is where the panel will be put.

<div id="time"></div>

Once all the divs are in place, you can write JavaScript to place the appropriate Pandemix panels.

<script>
    var timePanel = new pandemix.TimePanel; //create panel
    timePanel.placePanel({target: "#time"}); //place panel using a CSS selector
</script>

Then, if the default styling doesn't suit you, some CSS editing:

.timeLine {
    width: 750px;
    height: 25px;
    cursor: crosshair;
}

And that is it. Your page now has a functioning interactive timeline to explore your data temporally. Some panels require additional options and considerations based on their complexity and what data they depend on, but pattern remains the same.

Panel listing

Tree panel

Phylogenetic tree with branch lengths. The topology of the tree can be drag-selected and leaves can be click-selected, including the usual behavior when shift or ctrl (cmd on Mac) keys are held down.

var treePanel = new pandemix.TreePanel;
treePanel.placePanel("#tree1");
treePanel.initializePanelData({file: "data/tree1.json", color: "red"});

file - tree file in JSON format [need to specify format]
color - CSS color expression that will be associated with this tree. If no color is provided, one of 60 colors will be assigned from a color wheel, however these become increasingly hard to distinguish as more trees are added.

Time panel

Timeline that spans from the earliest date to the latest date as found among loaded tree panels. A time period can be selected in the timeline, this same period will highlight in tree panels and leaves that fall into this period will be highlighted. The time slider can be dragged. This will draw a vertical line in all tree panels corresponding to the same date. Map panel layers like the bubble chart layer and virus particle layers will display the geographical distribution of viruses for the selected date. Also, any “date-calendar” class spans will display the selected date.

var timePanel = new pandemix.TimePanel;
timePanel.placePanel({target: "#globalTime"});

target - target div

Trait selection panel

Selection panel for properties by which trees or map features can be colored by. Available options are loaded from metadata in tree files; the panel looks for naming patterns that look like someTrait.fullSet. The tree colors are loaded as well. Coloring legend is displayed in the legends panel.

var traitSelectionPanel = new pandemix.TraitSelectionPanel;
traitSelectionPanel.placePanel({target: "#traitSelection"});

target - target div

Legend panel

Color legend panel. The trait selection panel controls which property is colored for. Most properties will be assigned colors automatically from a HSB color wheel but colors can also be provided when adding data, like tree colors. Rows can be clicked to turn a color on or off, unless it is a manually set color.

var legendPanel = new pandemix.LegendPanel;
legendPanel.placePanel({target: "#legend"});

target - target div

Map panel

Leaflet based map panel with various overlays. The map can be panned and zoomed and overlay visibilty can be toggled on or off. When adding multiple layers the .addLayer(...) calls return the panel itself so these calls can be chained one after the other. Map layers will appear in the order that they were added unless a zIndex argument is provided.

var mapPanel = new pandemix.MapPanel;
mapPanel.placePanel({target: "map", initCoords: [34, 104], initZoom: 4});

target - target div
initCoords - initial center coordinates of map
initZoom - initial zoom level of map

Most overlays will require some additional data. Currently Pandemix supports adding a GeoJSON file with country and region outlines or a CSV file with location names and the coordinates of that location's centroid.

mapPanel.loadContours(contourFile)
        .loadCentroids(centroidFile);

If no centroid file is provided on the .loadCentroids call, centroids will be calculated from the contours and given the region's name.

Info display

Adds an info display popup in the bottom left of the map. The contents of the popup are determined by the string creation function passed by the user. Since this just edits the html content of the div, you can use html elements to style the output.

mapPanel.addInfoDisplay(function(d) {return "<h4>" + d.location + "</h4>" + d.treeName + " - " + d.number});

Currently only the bubble chart layer responds to this. As such the available data items are:

d.location - location name associated with the bubble
d.treeName - name of the tree the bubble belongs to
d.number - number of viruses represented by the bubble

Region outline layer

Contours of geographical bodies. Can be clicked to highlight tree leaves from the location. Requires loaded contours.

mapPanel.addLayer({layerType: pandemix.map.regionOutlineLayer, name: "Regions"});

layerType - type of layer to add
name - name that appears in layer toggle control

Locations layer

Draws a circle on centroid locations. Circles can be sized according to the count of leaves in that location.

mapPanel.addLayer({layerType: pandemix.map.locationLayer, name: "Locations", displayedProperty: "location", unitRadius: 1});

layerType - type of layer to add
name - name that appears in layer toggle control
displayedPropert - the string matching to location in tree data files
unitRadius - radius in pixels corresponding to one count at minimal zoom
minRadius - minimum radius in pixels at minimal zoom
maxRadius - maximum radius in pixels at minimal zoom

Note that setting a minimum or maximum radius disrupts interpretation on data visually. For example, one circle twice as big as another might not represent twice as many counts if the smaller one is forced to take a minimum radius.

Bubble chart layer

Draws circles sized corresponding to the number of virus mutations that exist at a selected time. The circles (or bubbles) repel each other so, when zoomed out, the bubbles won't center exactly around the centroid they belong to. Bubbles are colored according to which tree they represent.

mapPanel.addLayer({layerType: pandemix.map.bubbleChartLayer, name: "Bubble chart", unitRadius: 3});

layerType - type of layer to add
name - name that appears in layer toggle control
unitRadius - radius in pixels corresponding to one count at minimal zoom
chargeDensity - controls how strongly the particles repel each other
minRadius - minimum radius in pixels at minimal zoom
maxRadius - maximum radius in pixels at minimal zoom

Note that setting a minimum or maximum radius disrupts interpretation on data visually. For example, one circle twice as big as another might not represent twice as many counts if the smaller one is forced to take a minimum radius.

Bubble transition layer

Animates geographical transitions if the virus parent has been traced to a different location than where it spawns. Best used together with the bubble chart layer and placed underneath it (called first). These transitions work both when moving forward and backward in time. Bubbles are colored according to which tree they represent.

mapPanel.addLayer({layerType: pandemix.map.bubbleTransLayer, name: "Bubble transitions", radius: 2});

layerType - type of layer to add
name - name that appears in layer toggle control
radius - radius in pixels of transition particle at minimal zoom

Virus particle layer

A combination of bubble chart and bubble transition layers. Displays each node in the current selection as an individual circle at the nodes location. When time moves forward, the particles move from location to location and split according to the phylogenetic tree they represent. When moving back in time, transitions are not animated and particles simply dissapear and appear as appropriate. Particles are colored according to the tree they represent. Particles from a single tree repel each other but not particles from other trees so they may overlap in which case the bubble chart might be a better choice. Each tree appears on a separate layer.

mapPanel.addLayer({layerType: pandemix.map.virusParticleLayer, treePanel: treePanel, radius: 3});

layerType - type of layer to add
name - name that appears in layer toggle control
treePanel - reference to the tree panel this layer should represent
chargeDensity - controls how strongly the particles repel each other
radius - radius in pixels of virus particle at minimal zoom

Tree layer

Draws great arcs that mirror the links on the represented tree.

mapPanel.addLayer({layerType: pandemix.map.treeLayer, treePanel: treePanel, color: treePanel.getColor()});

layerType - type of layer to add
name - name that appears in layer toggle control
treePanel - reference to the tree panel this layer should represent
color - color of the tree links

Additional components

Pandemix provides some additional control components that are not directly parts of any one panel.

Zoom button

Vertically expands all tree panels.

pandemix.addGlobalZoomButton({target: "#zoom", zoomAmount: 1});

target - target div
zoomAmount - by how much the scale of the trees changes each click. Default is 0.5

Play/Pause button

Advances the time slider automatically. Useful for things like bubble chart and virus particle map layers.

pandemix.addPlayPauseButton({target: "#playPause", updateInterval: 200, updateStep: 10});

target - target div
updateInterval - time between each step forward in time in milliseconds. Default is 200
updateStep - amount of time the slider moves each update in days. Default is 10

Search box

Searches for the entered text substring in leaf names.

pandemix.addSearchBox({target: "#search"});

target - target div

Color box

Colors selected leaves. The entered text is interpreted as a CSS color, invalid expressions return the selection to their default colors.

pandemix.addColorPicker(target: "#color"});

target - target div

Date span

Any spany with the class date-calendar will be replaced by the selected date.

<span class="date-calendar"></span>