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.

• Default tip labelling is the sample / strain name (node.name)

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”
tip_label	What attribute (in ‘node_attrs’) to use as tip (node) labels	“country”
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
gmax	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
tl	Tip label to display	tl=country
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).

Measurements panel URL query options

The following query options are specifically for the measurements panel.

Key	Description	Example(s)
m_collection	Specify which collection to display	m_collection=h3n2_ha_cell_hi
m_display	Toggle measurements display between mean and raw	m_display=mean or m_display=raw
m_groupBy	Specify group by field to use	m_groupBy=reference_strain
m_overallMean	Show or hide the overall mean display	m_overallMean=show or m_overallMean=hide
m_threshold	Show or hide the threshold(s)	m_threshold=show or m_threshold=hide
mf_<field_name>	Filters for the measurements data. Multiple values for the same field are specified by multiple query params	mf_reference_strain=A/Alabama/5/2010 mf_clade_reference=145S.2&mf_clade_reference=158N/189K