lukas-eu
commented
4 years ago I would like to take over this issue but with a slightly modified goal: Enable graph zooming and navigation via scrolling/buttons and "grabbing" the graph (analogous to the map view)
In the context of this COVID-19 themed hackathon we formed a team to support open-source visualization tools for researchers. Specifically, one of our team members who is connected to the research community requested for the tree zooming to be more arbitrary/smooth overall.
jameshadfield
Motivating user story
John is interested in the hCoV-19 strains circulating in Washington State. He clicks the base node of the primary Washington State clade to zoom into that phylogenetic context (shown below). Next, John wants to view the Washington clade in the context of its sibling clades. He cannot zoom out from the current context by a single step up the tree. He has to click “Reset Layout” to return to the whole tree view, find his place in the tree again, and click the appropriate node for the ancestor of the Washington clade’s node.
Proposed solution
Provide an interface to allow users to “zoom out” of the tree in steps (or “step up the tree toward the root”).
The definition of a “step” up the tree can differ depending on the selected “Branch Length” mode. The figure above shows the “divergence” view of the tree where multiple strains are identical to their ancestral node (also known as a “polytomy”). For example, USA/WA1/2020 and Fujian/8/2020 and the ancestral node all have 3 mutations from the root of the tree. One step up the tree will take the user to the parent node of the ancestral node in the view above.
If the user has selected the “time” branch length view, they will see a tree like the one below instead.
If the user zoomed into the ancestral node of the USA/WA1/2020 sample, they would see:
One step up the tree from that node would be:
Proposed implementation ideas
Add an affordance to the root (or left-most ancestral) node in the current view to alert users that they can step up the tree by clicking something (e.g., the root again, or a nearby button, etc.).
Add a left arrow button (like https://fontawesome.com/icons/arrow-circle-left) that would allow the user to step up the tree once per click.
Consider implementing one “step” based on the divergence view of the tree regardless of the currently selected branch length view. This implementation could be more biologically relevant and easier to actually implement in the existing tree component. In this implementation, one step up from the zoomed in view of USA/WA1/2020 and Fujian/8/2020 above would look like the following (where USA/WA1/2020 is the earliest large red circle):
This is because the divergence values of USA/WA1/2020 and the other intermediary ancestral nodes shown in the time view are identical.
Alternately, consider implementing one step as a delta of the existing branch length view (e.g., divergence of 1 or time of 1 month).