Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Visualization tools #9

Open
gvegayon opened this issue Oct 18, 2017 · 0 comments
Open

Visualization tools #9

gvegayon opened this issue Oct 18, 2017 · 0 comments

Comments

@gvegayon
Copy link
Member

Web-based

  • Suggested by Paul Thomas, we can use iTOL. Seems to have API.

  • This is a javascript SVG based visualization tool jsPhyloSVG. Seems to have API, and moreover, suitable to be used with Shiny. Elsevier uses this. So far, this is the tool that I like the most.

  • SILVA Tree Viewer is a webapp.

  • TreeLink is a webapp.

  • PhyD3 makes interactive visualizations. Suitable for Shiny.

In R

  • The ape::plot.phylo function has several options that I was not aware of. Now that I realized that the coordinates of the nodes are stored in .PlotPhyloEnv$last_plot.phylo as xx and yy, I can use this as input to create more personalized visualizations.

  • The ggtree R package, currently used here, is not working properly when handling the annotations.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@gvegayon