diff --git a/docs/advanced-functionality/view-settings.rst b/docs/advanced-functionality/view-settings.rst index 00c152423..b453a1e77 100644 --- a/docs/advanced-functionality/view-settings.rst +++ b/docs/advanced-functionality/view-settings.rst @@ -17,7 +17,7 @@ Auspice has some hardcoded defaults, largely for historical reasons. Each of the - 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`) +- Default tip labelling is the sample / strain name (``node.name``) Dataset (JSON) configurable defaults ------------------------------------ diff --git a/docs/releases/v2.rst b/docs/releases/v2.rst index abe58e855..f7b03fefc 100644 --- a/docs/releases/v2.rst +++ b/docs/releases/v2.rst @@ -83,7 +83,16 @@ v1 Auspice JSONs used 0-based starts for the gene positions and ``1``/``-1`` for Changes to how node data is stored ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Each tree node (internal & terminal) can now contain the following properties \* ``name`` (required) -- formerly this was ``strain`` \* ``node_attrs`` -- attributes associated with the node (sequence, date, location) as opposed to changes from one node to another. \* Node attributes can now be objects and contain confidence information if available. \* A ``hidden`` node attribute can control Auspice's display of the node \* Author information is now contained under the ``author`` key, and the ``author_info`` dictionary is no longer present in the JSON. \* ``branch_attrs`` -- attributes associated with the branch from the parent node to this node, such as branch lengths, mutations, support values \* ``branch_attrs.mutations`` -- both AA & nucleotide mutations are now defined in the same object. \* ``children`` (unchanged) +Each tree node (internal & terminal) can now contain the following properties + +* ``name`` (required) -- formerly this was ``strain`` +* ``node_attrs`` -- attributes associated with the node (sequence, date, location) as opposed to changes from one node to another. +* Node attributes can now be objects and contain confidence information if available. +* A ``hidden`` node attribute can control Auspice's display of the node +* Author information is now contained under the ``author`` key, and the ``author_info`` dictionary is no longer present in the JSON. +* ``branch_attrs`` -- attributes associated with the branch from the parent node to this node, such as branch lengths, mutations, support values +* ``branch_attrs.mutations`` -- both AA & nucleotide mutations are now defined in the same object. +* ``children`` (unchanged) Colorings, geographic resolutions, and defaults ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^