Hi Liam, Absolutely fantastic, I can see this being useful on multiple occasions, particularly as it takes another step towards being more explicit about our uncertainty in ASRs for continuous traits (especially when traitgrams are not ideal for whatever reason). If you get time I would suggest turning that code into a function to add to phytools as it might be broadly useful for many researchers, but for my own purposes the code you have added to the blog is perfectly fine.
Best wishes, Kev ________________________________________ From: Liam J. Revell [liam.rev...@umb.edu] Sent: 27 February 2017 21:57 To: Arbuckle, Kevin; R phylo list Subject: Re: [R-sig-phylo] Plotting uncertainty in continuous ASR Hi Kevin. I now show one way to do this here: http://blog.phytools.org/2017/02/more-on-adding-error-bars-to-contmap.html. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 2/27/2017 2:32 PM, Arbuckle, Kevin wrote: > Hi Liam, > > Thank for that, definitely much quicker than I could have figured it out. The > only other thing I'd do would be have the length varying to reflect the range > of the estimates, giving an immediate visual display of both the range of > variation and the actual values encompassed, but that's something that can be > tailored relatively easily from that code so thanks again. > > Kev > > ________________________________________ > From: Liam J. Revell [liam.rev...@umb.edu] > Sent: 27 February 2017 19:13 > To: Arbuckle, Kevin; r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] Plotting uncertainty in continuous ASR > > Hi Kevin. > > This is not automatic - but it is indeed fairly easy to do using > phytools. To be honest, I thought this would look terrible - but it > actually looks much better than I expected, at least for a relatively > small tree. I have posted a demo to my blog here: > http://blog.phytools.org/2017/02/adding-colorful-error-bars-to-internal.html. > > All the best, Liam > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 2/27/2017 11:16 AM, Arbuckle, Kevin wrote: >> Hi all, >> >> I was wondering about plotting the output of an ancestral state >> 'reconstruction' of a continuous trait while incorporating at least some of >> the uncertainty around the estimates. >> >> One approach I thought of was to map the ASR onto a tree in a standard way, >> then at each node have essentially a mini-legend that is of a length >> reflecting the width of the confidence interval of the estimate at that >> node, and is coloured on the same colour-scale as the overall tree legend. >> For instance, if the colour scheme for the tree goes from blue through >> yellow to red as the value increases, then a node with a relatively precise >> and high estimate will have a short bar only ranging through different >> shades of red, whereas a highly uncertain low estimate will have a wider bar >> coloured from (say) dark blue to orange/light red. I hope that description >> makes sense. >> >> I was wondering if anyone is aware of a function that already implements >> such an approach, otherwise I'll try to put one together myself. I am aware >> of phytool's fancyTree(type="phenogram95") as a way of incorporating >> uncertainty into a plotted ASR for continuous traits. However, this often >> results in difficulty in distinguishing different nodes where estimates are >> similar and also does not lend itself easily to, for instance, plotting pie >> charts representing discrete trait ASRs onto a tree mapped with a continuous >> trait. Hence I can imagine a more general approach as above but don't want >> to duplicate effort if a function already exists (and also if others feel >> this is a useful idea it can be added to existing packages If I share it as >> above). >> >> Best wishes, >> Kev >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> > _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
