flag to control ladderize about ggtree

[GuangchuangYu]

Hi, you can use the right parameter, by default right=TRUE and the direction is increasing.
If you want decreasing order, use right=FALSE.

An example can be found in http://ygc.name/2015/04/01/an-example-of-drawing-beast-tree-using-ggtree/.

[michaelalfaro]

Hi Yu,

Thanks for making ggtree! I spent most of the day with it and am very impressed. I was wondering if you could answer two questions for me?

1. Is it possible to reverse the timescale in theme_tree2 so that the oldest ages are at the root and 0 is at the present?

2. is there a way to control the size of the tree relative to the size available for tip names and image annotations? I would like to have control of the x axis of the tree figure so I could shrink it a bit and leave more room to taxon names etc.

Thanks for any help!

Mike

On Oct 19, 2015, at 8:28 AM, Guangchuang Yu [email protected] wrote:

Hi, you can use the right parameter, by default right=TRUE and the direction is increasing.
If you want decreasing order, use right=FALSE.

An example can be found in http://ygc.name/2015/04/01/an-example-of-drawing-beast-tree-using-ggtree/ http://ygc.name/2015/04/01/an-example-of-drawing-beast-tree-using-ggtree/.

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Reply to this email directly or view it on GitHub #18 (comment).

[GuangchuangYu]

Q1

p <- ggtree(rtree(30))
p$data$x <- p$data$x - max(p$data$x)
p

Q2

annotating with image is always relative to the drawing canvas, so the answer is yes.

But for tip names, we can't control their size relative to the tree or vice verse, see my answer to the question.

If you just want to allocate more space for tip names, just use xlim to get more space.

[michaelalfaro]

thanks very much!!!

On Oct 21, 2015, at 7:41 PM, Guangchuang Yu [email protected] wrote:

Q1

p <- ggtree(rtree(30))
p$data$x <- p$data$x - max(p$data$x)
p
Q2

annotating with image http://ygc.name/2015/08/01/ggtree-annotate-phylogenetic-tree-with-local-images/ is always relative to the drawing canvas, so the answer is yes.

But for tip names, we can't control their size relative to the tree or vice verse, see my answer to the question https://support.bioconductor.org/p/72398/.

If you just want to allocate more space for tip names, just use xlim to get more space.

—
Reply to this email directly or view it on GitHub #18 (comment).

[michaelalfaro]

Hi Guanchuang,

Is there a way to adjust the position of geom_nodepoints? I tried something like this but I don’t think the points are moving….

ggtree(beast) + geom_nodepoint(aes(label = bootstrap), vjust=.1, hjust=-10, size = 2)

thanks very much!

On Oct 21, 2015, at 7:41 PM, Guangchuang Yu [email protected] wrote:

Q1

p <- ggtree(rtree(30))
p$data$x <- p$data$x - max(p$data$x)
p
Q2

annotating with image http://ygc.name/2015/08/01/ggtree-annotate-phylogenetic-tree-with-local-images/ is always relative to the drawing canvas, so the answer is yes.

But for tip names, we can't control their size relative to the tree or vice verse, see my answer to the question https://support.bioconductor.org/p/72398/.

If you just want to allocate more space for tip names, just use xlim to get more space.

—
Reply to this email directly or view it on GitHub #18 (comment).

[GuangchuangYu]

you can't move the point.

It seems you want to label bootstrap value, try using geom_text.

[michaelalfaro]

ok thanks. I wanted to use a symbol for the bootstrap values and another symbol for the posteriors….

On Nov 3, 2015, at 6:14 PM, Guangchuang Yu [email protected] wrote:

you can't move the point.

It seems you want to label bootstrap value, try using geom_text.

—
Reply to this email directly or view it on GitHub #18 (comment).