Re: [R-sig-phylo] Adding a custom legend underneath a phylo plot with coloured tips
This is what finally worked for me for setting up the plot with the
legend how I wanted:
(result is in attached PDF)
Perhaps some of you will find it useful for your own work...
#Zeileis et al.'s function for drawing palettes
pal <- function(col, border = "light gray", ...)
{
n <- length(col)
plot(0, 0, type="n", xlim = c(0, 1), ylim = c(0, 1), axes = FALSE,
xlab = "", ylab = "", ...)
rect(0:(n-1)/n, 0, 1:n/n, 1, col = col, border = border)
}
library(phytools)
library(colorspace)
setwd("C:/EXTRACT_LEAF_TRAITS/TRAITVAR_RESULTS/")
MYTREE = read.nexus("s4970_t500_1.nex")
MYDATA = read.csv("s4970_t500_1.csv")
MYCOLRANGE = read.table("colorrange2.txt",header=F,sep="\t")
MCRD = dim(MYCOLRANGE)
#PAL = diverge_hcl(MCRD[1],h=c(246,40),c=96)
#PAL = heat_hcl(MCRD[1],c=c(80,30),l=c(30,90),power=c(1/5,1.5))
#PAL = heat.colors(MCRD[1])
PAL = rainbow(MCRD[1])
MYCOLRANGE[,3] = PAL #to coerce palette values to character instead of factor
tips = getExtinct(MYTREE,tol=0.01)
neo_tree = drop.tip(MYTREE,tips)
EXT_TIP_TRAITS = MYDATA[which(MYDATA[,3]==T),]
TIPLABCOLS = vector(mode="character",length=dim(EXT_TIP_TRAITS)[1])
for (i in 1:length(neo_tree$tip.label))
{
CurrTVal = EXT_TIP_TRAITS[i,2]
#message(CurrTVal)
for (j in 1:dim(MYCOLRANGE)[1]){
#message(MYCOLRANGE[j,1])
#message(MYCOLRANGE[j,2])
#message(MYCOLRANGE[j,3])
if ((CurrTVal >= MYCOLRANGE[j,1]) && (CurrTVal <= MYCOLRANGE[j,2])){
#message(MYCOLRANGE[j,3])
TIPLABCOLS[i] = MYCOLRANGE[j,3]
break
}
}
}
BINVALCHRVEC = vector(mode="character")
for (n in 1:dim(MYCOLRANGE)[1]) {
BINVALCHR = paste(as.character(MYCOLRANGE[n,1])," - ",
as.character(MYCOLRANGE[n,2]),sep="")
BINVALCHRVEC = c(BINVALCHRVEC,BINVALCHR)
}
colours = MYCOLRANGE[,3]
dev.off()
layout(rbind(1,2), heights=c(5.5,2.5))
layout.show(n=2)
par(mar=c(1, 0.25, 1, 0.25))
plot.phylo(neo_tree,type="phylogram",root.edge=TRUE, no.margin=FALSE,
show.tip.label=FALSE)
tiplabels(pch=22, col=TIPLABCOLS, bg=TIPLABCOLS, cex=0.3)
par(mar=c(0, 0, 0, 0))
# c(bottom, left, top, right)
plot.new()
legend("left", "groups", bty='n', legend=BINVALCHRVEC, ncol=6,
col=MYCOLRANGE[,3], bg = MYCOLRANGE[,3], pch =
rep(15,length(MYCOLRANGE[1:3])), cex=0.59)
cheers,
Gabe
On 10/28/16, Gabriel Yedid <gyedi...@gmail.com> wrote:
> Hello all,
>
> I have a phylo plot where each tip of the tree has a certain trait
> value associated with it. The trait is represented by a
> continuously-valued number bounded by x and y (2.0 and 15.0 for these
> purposes). In order to make display tractable, the values are binned,
> with each bin being assigned one colour from a sequential palette.
>
> I have been able to display the tree as I want, with each tip getting
> a single coloured square that represents its trait value (within the
> bin range), but now I want to create a custom legend and put it below
> the phylo plot. I know how to divide the plot window to position the
> legend there, but not how to assemble and display the legend itself.
>
> What I want is to have a coloured square representing the bin, with
> text showing the bin's lower and upper limits to the right of the
> square,
>
> [ ] bin_a_lower - bin_a_upper [ ] bin_d_lower - bin_d_upper
> [ ] bin_b_lower - bin_b_upper [ ] bin_e_lower - bin_e_upper
> [ ] bin_c_lower - bin_c_upper
>
> Each of the [ ] would get a different colour specified by the hex
> codes in the palette's character vector.
>
> Does anybody know how to put the legend together from elements that
> would already be in the workspace? (the palette vector, the bin limit
> values, etc.) Is there a way to do it with the default legend()
> function that I just don't know, or does it have to be assembled
> piece-by-piece?
>
> Alternatively, how would I get a colourbar to display in that same
> space below the plotted tree?
>
> cheers,
>
> Gabe
>
Rplot03.pdf
Description: Adobe PDF document
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[R-sig-phylo] Adding a custom legend underneath a phylo plot with coloured tips
Hello all, I have a phylo plot where each tip of the tree has a certain trait value associated with it. The trait is represented by a continuously-valued number bounded by x and y (2.0 and 15.0 for these purposes). In order to make display tractable, the values are binned, with each bin being assigned one colour from a sequential palette. I have been able to display the tree as I want, with each tip getting a single coloured square that represents its trait value (within the bin range), but now I want to create a custom legend and put it below the phylo plot. I know how to divide the plot window to position the legend there, but not how to assemble and display the legend itself. What I want is to have a coloured square representing the bin, with text showing the bin's lower and upper limits to the right of the square, [ ] bin_a_lower - bin_a_upper [ ] bin_d_lower - bin_d_upper [ ] bin_b_lower - bin_b_upper [ ] bin_e_lower - bin_e_upper [ ] bin_c_lower - bin_c_upper Each of the [ ] would get a different colour specified by the hex codes in the palette's character vector. Does anybody know how to put the legend together from elements that would already be in the workspace? (the palette vector, the bin limit values, etc.) Is there a way to do it with the default legend() function that I just don't know, or does it have to be assembled piece-by-piece? Alternatively, how would I get a colourbar to display in that same space below the plotted tree? cheers, Gabe ___ 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] Implementation of Mir et al.'s (2013) tree balance index?
Hello all, Is there any R implementation yet of the tree balance metric described in: Mir, Arnau, Francesc Rosselló, and Lidia Rotger. "A new balance index for phylogenetic trees." Mathematical biosciences 241.1 (2013): 125-136. cheers, Gabe ___ 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] Problem loading phytools on Mac
Hello list, Has anyone else experienced the following error when trying to load phytools on a Mac, even though it seems to have been successfully installed? Note that this problem doesn't seem to be with phytools itself, but with rgl: library(phytools) Loading required package: ape Loading required package: maps Error : .onLoad failed in loadNamespace() for 'rgl', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/rgl/libs/rgl.so': dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/rgl/libs/rgl.so Reason: image not found Error: package or namespace load failed for ‘phytools’ I haven't experienced this problem using phytools on a PC. Anybody know what gives here? cheers, Gabe ___ 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] Problem processing trees with more nodes than tips...
Hello all, I'm having a curious problem in that I have trees that seem to have more nodes than tips. They're part of a time series of trees (not generated with an R package) that I'm reading in and doing tree shape analyses of. Not all of the trees have this problem, but once it crops up it persists in all trees generated after that point. The tree file (in Nexus format) is read in OK, but when I try to plot it I see: plot(INTREE, show.tip.label=FALSE) Error in plot.phylo(INTREE, show.tip.label = FALSE) : tree badly conformed; cannot plot. Check the edge matrix. summary(INTREE) Phylogenetic tree: INTREE Number of tips: 5796 Number of nodes: 5797 Branch lengths: mean: 9.617864 variance: 149.9489 distribution summary: Min. 1st Qu. Median 3rd Qu.Max. 0.000 2.480 6.213 12.740 188.200 Root edge: 17.5434 First ten tip labels: taxa_1000 taxa_10001 taxa_10002 taxa_10003 taxa_10004 taxa_10005 taxa_10006 taxa_10008 taxa_10009 taxa_10019 No node labels. And when I try to drop all of the extinct tips of the tree, all tips are dropped! What could be causing this behaviour? How can it be fixed (in R)? cheers, Gabe ___ 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/
Re: [R-sig-phylo] Problem processing trees with more nodes than tips...
OK, I think I've figured out what the trouble is, it's a problem with the way the input Nexus files are being written. The trouble is with the data in the translation table. If I extract the Newick tree structure by itself, without the translation labels, the tree can be read and processed normally (though of course the tip labels are anonymous now). Is there some way of getting read.nexus() to ignore the translation table? cheers, Gabe On Wed, Nov 12, 2014 at 7:03 PM, Gabriel Yedid gyedi...@gmail.com wrote: Hello all, I'm having a curious problem in that I have trees that seem to have more nodes than tips. They're part of a time series of trees (not generated with an R package) that I'm reading in and doing tree shape analyses of. Not all of the trees have this problem, but once it crops up it persists in all trees generated after that point. The tree file (in Nexus format) is read in OK, but when I try to plot it I see: plot(INTREE, show.tip.label=FALSE) Error in plot.phylo(INTREE, show.tip.label = FALSE) : tree badly conformed; cannot plot. Check the edge matrix. summary(INTREE) Phylogenetic tree: INTREE Number of tips: 5796 Number of nodes: 5797 Branch lengths: mean: 9.617864 variance: 149.9489 distribution summary: Min. 1st Qu. Median 3rd Qu.Max. 0.000 2.480 6.213 12.740 188.200 Root edge: 17.5434 First ten tip labels: taxa_1000 taxa_10001 taxa_10002 taxa_10003 taxa_10004 taxa_10005 taxa_10006 taxa_10008 taxa_10009 taxa_10019 No node labels. And when I try to drop all of the extinct tips of the tree, all tips are dropped! What could be causing this behaviour? How can it be fixed (in R)? cheers, Gabe ___ 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] problem dropping extinct taxa from large tree
Hello all, I am trying to drop extinct taxa from a large phylogeny generated with a non-R-based tree simulation program. The tree was saved in a Nexus file which was read in with read.nexus. It's quite large--10911 leaves, but only 2055 are alive i.e. lineages that survived to the end of the simulation. It's these lineages I want to keep around for further analysis. I've tried both the drop.fossil (from APE) and drop.extinct(from geiger) functions, but both of them give problems. If I use the customary low tolerance for either of these functions, drop.fossil produces the following error: INTREE_EXTANT = drop.fossil(INTREE, tol=1e-6) Error in xmat[, 1] : incorrect number of dimensions Lowering the tolerance value to 1e-4 trims off some of the living tips I wanted kept (the resulting tree is smaller than it's supposed to be). drop.extinct just seems to hang and doesn't return even after about 10 minutes, no matter what tolerance value I supply. Is there some other way I can remove extinct lineages from a large tree like this? cheers, Gabe ___ 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] Meaning of output from phytools findMRCA ?
Hi all, I'm trying to use picante and phytools in combination to analyze particular aspects of communities of digital organisms. I use picante to read in the data for community, trait, and phylogeny data, and make sure everything is matched up properly. My interest in using phytools (at least right now) is using the findMRCA function to find the MRCA of groups of organisms with particular phenotypic traits. The data look like this: TRAIT1 TRAIT2 TRAIT3 TRAIT4 TRAIT5 TRAIT6 TRAIT7 TRAIT8 TRAIT9 F3666295 0167 0 83 0 81 0 0 0 F3664184 0165 0 83 0 82 0 0 0 F3665912121 42 0 41 0 0 0 0 0 F3665920 0165 0 83 0 81 0 0 0 F3654948 0 0 0 82 0 80 0 0 0 F3663933 81 82 0 82 0 80 0 0 0 TRAIT10 PHENO F3666295 15.376584 F3664184 15.186084 F3665912 14.709322 F3665920 15.209384 F3654948 15.023380 F3663933 14.872186 The row names are the unique IDs of the genotypes in the population. Traits 1 through 10 are traits reflecting various aspects of the phenotype; the trait called PHENO is a numerical summary of traits 1-9. It's this that I want to use as the index for finding MRCAs (e.g. find the MRCA of all organisms with PHENO = 84) After having read in and cleaned up everything with picante, I attach(TRAITS.EDITED.MATCHED.WORK$data) #this is the object of matched-up tree + data produced by picante #names(TRAITS.EDITED.MATCHED.WORK$data) SUBJECT = TRAITS.EDITED.MATCHED.WORK$data[PHENO==84,] #just for example, this extracts the vector of tip labels needed by findMRCA findMRCA(TRAITS.EDITED.MATCHED.WORK$phy,tips= row.names(SUBJECT),type=node) findMRCA(TRAITS.EDITED.MATCHED.WORK$phy,tips= row.names(SUBJECT),type=height) This produces output like: findMRCA(TRAITS.EDITED.MATCHED.WORK$phy,tips= row.names(SUBJECT),type=node)[1] 1322 findMRCA(TRAITS.EDITED.MATCHED.WORK$phy,tips= row.names(SUBJECT),type=height)[1] 73681 What exactly is the meaning of these numbers? The vector of node labels for the associated tree doesn't have that many elements, so what does node = 1322 mean? Is it actually meaningful, or is this some kind of error? What I really want, in this case, is the name of the node, which has a unique genotype ID like those shown above. And is the node height measured relative to the root, or to the tips? Any help is much appreciated! cheers, Gabe [[alternative HTML version deleted]] ___ 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] ATTN Liam Revell: please contact me off-list
This is a shout-out to Liam Revell: I've been trying to contact you off-list but I'm not sure if my messages have been getting through. Please contact me at gyedi...@gmail.com. We now return you to your regularly scheduled programming... cheers, Gabe [[alternative HTML version deleted]] ___ 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/
