branch line thickness

[cool_a...@web.de]

Is it possible to make branches thicker if the node is supported by a bootstrap value greather than x?

[Yu, Guangchuang]

something like this:

ggtree(tr, aes(size=label > 80)) + scale_size_manual(values=c(1, .1))

On Mon, Jan 2, 2017 at 1:14 PM, <cool_a...@web.de> wrote:

Is it possible to make branches thicker if the node is supported by a bootstrap value greather than x?

--
You received this message because you are subscribed to the Google Groups "ggtree" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bioc-ggtree+unsubscribe@googlegroups.com.
To post to this group, send email to bioc-...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/bioc-ggtree/d33a7292-906b-4c7b-8a96-e1ada96f3457%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

--~--~---------~--~----~------------~-------~--~----~

Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong

Hong Kong SAR, China

www: https://guangchuangyu.github.io

-~----------~----~----~----~------~----~------~--~---

[cool_a...@web.de]

Unfortunately the branch thickness stays at 1 until it either hits a tip node or another node with >70, even if the next split has only a bootstrap value of <70.

Am Dienstag, 3. Januar 2017 04:31:12 UTC+1 schrieb Yu, Guangchuang:

something like this:

ggtree(tr, aes(size=label > 80)) + scale_size_manual(values=c(1, .1))

On Mon, Jan 2, 2017 at 1:14 PM, <cool_a...@web.de> wrote:

Is it possible to make branches thicker if the node is supported by a bootstrap value greather than x?

--
You received this message because you are subscribed to the Google Groups "ggtree" group.

To unsubscribe from this group and stop receiving emails from it, send an email to bioc-ggtree...@googlegroups.com.

To post to this group, send email to bioc-...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/bioc-ggtree/d33a7292-906b-4c7b-8a96-e1ada96f3457%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Yu, Guangchuang]

This is complicated, since tips don't have bootstrap value, and we need to assign parent status to tips.

require(ggtree)
## you need github version of ggtree and treeio

## treeio::read.newick can parse node label as separated support value.

x = read.newick('RAxML_Zingiberaceae.tre', node.label='support')
edge = x@phylo$edge
edge = as.data.frame(edge)
edge = edge[edge[,2] <= Ntip(x), ]

df = x@data
merge(df, edge, by.x="node", by.y="V1", all.x=F, all.y=T) -> df2
df3= df2[, c(3, 2)]
colnames(df3) = colnames(df)
x@data = rbind(df3, df)

ggtree(x, aes(size=I(support/100)))

To unsubscribe from this group and stop receiving emails from it, send an email to bioc-ggtree+unsubscribe@googlegroups.com.

To post to this group, send email to bioc-...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/bioc-ggtree/d31f632b-7d94-4bff-b2f7-89ff67088d63%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.