james hadfield

Scatterplots will not render nodes which don't define values for the selected `x` and `y` variables, however this information is not taken into account for the info-header "Showing X of...

Scatterplots do not zoom when data is filtered

1

Scatterplots, as implemented by #1310, do not "zoom" as expected when visibility update, e.g. with filtering. This is because filtering does not currently change the position of nodes in a...

Narratives cannot zoom to selected (tree panel)

4

**Context** [Auspice 2.21.0](https://github.com/nextstrain/auspice/blob/master/CHANGELOG.md#version-2210---20210106) introduced a "zoom to selected" button (via [PR 1257](https://github.com/nextstrain/auspice/pull/1257). This allows filtered trees to be zoomed to the subtree containing all the selected ("visible") tips. This zooming...

Scatterplot axis domains should dynamically update

1

This issue represents an observation from @huddlej in https://github.com/nextstrain/auspice/pull/1346#pullrequestreview-664992598 > [I wish that I could] filter tips to specific values in a category and have all other other values in...

Zoom to selected is stored as a URL query

4

When clicking "Zoom to selected" we now add a URL query `treeZoom=selected`, which is cleared upon the next zoom action. This allows us to load a page to a zoomed...

Following on from https://github.com/nextstrain/auspice/pull/1308 which allowed node attrs to be links, this allows them to load different datasets. The code here isn't well tested, but provides a starting point for...

entropy gene annotation

2

Overlapping genes are an issue. Our only example is "sGP" vs "GP" in Ebola. Will be worse with overlapping reading frames.

This updates the workflow to use augur after augur PR https://github.com/nextstrain/augur/pull/728 has been merged. It removes two rules from the workflow. In the situation where the ncov workflow is not...

Auspice testing data (get-data)

3

## Background This repo doesn't contain any datasets beyond some [very minimal examples to explain the dataset format](https://github.com/nextstrain/auspice/tree/master/examples). Instead we rely on the [get-data script](https://github.com/nextstrain/auspice/blob/master/scripts/get-data.sh) which downloads a slew of...

### Current Behaviour Load any tree and select a time slice such that (a) the root node is not selected and (b) the CA of filtered tips is not the...