export final tree with CI intervals

[fengyuchengdu]

Thanks for this great tool. I'm new to R and wondering if it allows to save the final tree with CI intervals, then I can, for example, drawing 95% CI bars in program like figtree or dragging it into itol, etc. So far I tried write.tree/nexus and it didn't incorperate CI values. Thanks.

[xavierdidelot]

Hi,

I think this should be possible if you use the recently added function as.treedata and then the function write.beast from the treeio package. You will need to have both packages ggtree and treeio installed, and the latest version of BactDating from github. Could you please give this a try and let me know if this works or not?

Best wishes, Xavier

[fengyuchengdu]

it worked. thanks

[xavierdidelot]

Great!

[fengyuchengdu]

Sorry to re-open this.

I followed the example "Application of BactDating on S. aureus ST239" and got the "res". Then I followed your suggestion as shown above (installed treeio and ggtree)

write.beast(as.treedata(res$tree)) however it didn't work as it did once before, instead it showed me the following (the last few lines) 51 51, 52 52, 53 53, 54 54, 55 55, 56 56, 57 57, 58 58 ; TREE * UNTITLED = [&R] Error in seq_len(nrow(yy)) : argument must be coercible to non-negative integer In addition: Warning messages: 1: Unknown or uninitialised column: 'node'. 2: In seq_len(nrow(yy)) : first element used of 'length.out' argument

treeio v1.11.2 ggtree v1.14.6

could you please help me fix this, many thanks.

[xavierdidelot]

Here's an example of how to use this functionality:

library(treedata)
library(ggtree)
res=bactdate(...)
l=as.treedata.resBactDating(res)
obj=methods::new('treedata',phylo=l[[1]],data=dplyr::tbl_df(as.data.frame(l[[2]])))
ggtree(obj) + geom_range(range='length_0.95_HPD', color='red', alpha=.6, size=2)

[fengyuchengdu]

Many thanks