ggtree: color-code multiple paraphyletic clades

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ggtree: color-code multiple paraphyletic clades

April Ettington
I've been using groupOTU to color paraphyletic clades in my tree based on
lists of tips, but I have multiple clades I want to highlight.  Is there
some way to use ggplot to indicate multiple paraphyletic clades?

Thank you

        [[alternative HTML version deleted]]

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Re: ggtree: color-code multiple paraphyletic clades

Rui Barradas
Hello,

You should post a reproducible example like the posting guide asks you to.
In the mean time, are you looking for [1], section Group Clades, by
package ggtree author? It even seems to be the package vignette.

[1]
https://bioconductor.riken.jp/packages/3.8/bioc/vignettes/ggtree/inst/doc/treeManipulation.html


Hope this helps,

Rui Barradas

Às 21:59 de 11/11/20, April Ettington escreveu:

> I've been using groupOTU to color paraphyletic clades in my tree based on
> lists of tips, but I have multiple clades I want to highlight.  Is there
> some way to use ggplot to indicate multiple paraphyletic clades?
>
> Thank you
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: ggtree: color-code multiple paraphyletic clades

April Ettington
Thank you, it seems the solution is to define the nodes in groupOTU using a
list of vectors.

On Thu, Nov 12, 2020 at 12:15 PM Rui Barradas <[hidden email]> wrote:

> Hello,
>
> You should post a reproducible example like the posting guide asks you to.
> In the mean time, are you looking for [1], section Group Clades, by
> package ggtree author? It even seems to be the package vignette.
>
> [1]
>
> https://bioconductor.riken.jp/packages/3.8/bioc/vignettes/ggtree/inst/doc/treeManipulation.html
>
>
> Hope this helps,
>
> Rui Barradas
>
> Às 21:59 de 11/11/20, April Ettington escreveu:
> > I've been using groupOTU to color paraphyletic clades in my tree based on
> > lists of tips, but I have multiple clades I want to highlight.  Is there
> > some way to use ggplot to indicate multiple paraphyletic clades?
> >
> > Thank you
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.