Web app for visualizing pathogen evolution

View Settings

View settings refer to things such as how we display the tree (radial? root-to-tip?), what panels we display (map? tree? both?), what colouring we are using etcetera. There are three ways these can be controlled:

  1. The defaults are configured by the dataset creators (and stored as “display defaults” in the dataset JSON). This allows
  2. Interacting with the visualisation (e.g. changing the color-by) modifies the view, and the URL is changed accordingly. For instance, change nextstrain.org/zika to have a color-by of author, and you’ll see the URL silently update to ?c=author. If you reload the page or share this URL, then the color-by is set via this URL.
  3. Narratives, in which the narrative author chooses different “views” for each page, are created by associating each page with a URL (see (2)) which defines a specific view into the data.

Auspice (hardcoded) defaults

Auspice has some hardcoded defaults, largely for historical reasons. Each of these can be overridden by the JSON display_defaults, and then the view can be further modified by the URL query (see below).

  • Default phylogeny layout is rectangular.
  • Default phylogeny distance measure is time, if available.
  • Default geographic resolution is “country”, if available.
  • Default colouring is “country”, if available.
  • Default branch labelling is “clade”, if available.

Dataset (JSON) configurable defaults

These are exported as the (optional) property of the dataset JSON meta.display_defaults (see JSON schema here). The defaults (as set here) will be what are displayed when the page is loaded with no URL queries, but be aware that URL queries (see below) can modify how the view looks. For instance, if you set display_defaults.color_by to country, but load the page with ?c=region then the view will be coloured by region.

Property Description Example
color_by Colouring “country”
geo_resolution Geographic resolution “country”
distance_measure Phylogeny x-axis measure “div” or “num_date”
map_triplicate Should the map repeat, so that you can pan further in each direction? Boolean
layout Tree layout “rect”, “radial”, “unrooted”, “clock” or “scatter”
branch_label Which set of branch labels are to be displayed “aa”, “lineage”
sidebar Should the sidebar start open or closed? “open” or “closed”
panels List of panels which (if available) are to be displayed [“tree”, “map”]
transmission_lines Should transmission lines (if available) be rendered on the map? Boolean
language Language to display Auspice in “ja”

Note that meta.display_defaults.panels (optional) differs from meta.panels (required), where the latter lists the possible panels that auspice may display for the dataset. See the JSON schema for more details.

See this in action:

For instance, go to nextstrain.org/flu/seasonal/h3n2/ha/2y and you’ll see how the colouring is “Clade” – this has been set via the display_defaults in the JSON.

URL query options

URL queries are the part of the URL coming after the ? character, and typically consist of key=value – for instance nextstrain.org/zika?c=author has a query with a key c and value author. Multiple queries are separated by the & character. All URL queries modify the view away from the default settings – if you change back to a default then that URL query will disappear.

Key Description Example(s)
c Colouring to use c=author, c=region
r Geographic resolution r=region
m Phylogeny x-axis measure m=div
l Phylogeny layout l=clock
scatterX Scatterplot X variable scatterX=num_date
scatterY Scatterplot Y variable scatterY=num_date
branches Hide branches branches=hide
regression Show/Hide regression line regression=hide, regression=show
transmissions Hide transmission lines transmissions=hide
lang Language lang=ja (Japanese)
dmin Temporal range (minimum) dmin=2008-05-13
dmax Temporal range (maximum) dmax=2010-05-13
f_<name> Data filter. Multiple values per key are , separated. f_region=Oceania
gt Genotype filtering  
d List of panels to display, , separated d=tree,map
p Panel layout (buggy!) p=full, p=grid
gmin Entropy panel zoom (minimum) bound gmin=1000
gmin Entropy panel zoom (maximum) bound gmax=2000
animate Animation settings  
n Narrative page number n=1 goes to the first page
s Selected strain s=1_0199_PF
branchLabel Branch labels to display branchLabel=aa
showBranchLabels Force all branch labels to be displayed showBranchLabels=all
label Labeled branch that tree is zoomed to label=clade:B3, label=lineage:relapse
clade DEPRECATED Labeled clade that tree is zoomed to clade=B3 should now become label=clade:B3
sidebar Force the sidebar into a certain state sidebar=closed or sidebar=open
legend Force the legend into a certain state legend=closed or legend=open
onlyPanels Do not display the footer / header. Useful for iframes. onlyPanels
ci Display confidence intervals on the tree. ci

See this in action:

For instance, go to nextstrain.org/flu/seasonal/h3n2/ha/2y?c=num_date&d=tree,map&m=div&r=region and you’ll see how we’ve changed the coloring to a temporal scale (c=num_date), we’re only showing the tree & map panels (d=tree,map), the tree x-axis is divergence (m=div) and the map resolution is region (r=region).