Re: [R-sig-phylo] Adding a custom legend underneath a phylo plot with coloured tips
Hi Gabriel.
For future reference, phytools has a couple of functions that could be
useful. add.simmap.legend (e.g.,
http://www.phytools.org/blog/18Nov16-post.png), used on my blog here:
http://blog.phytools.org/2016/11/updates-to-permit-user-control-of-line.html
and add.color.bar (e.g.,
http://blog.phytools.org/2015/06/customizing-your-contmap-style.html,
also vertical:
http://blog.phytools.org/2016/08/vertical-legend-in-contmap-style-plots.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 11/18/2016 10:57 AM, Gabriel Yedid wrote:
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 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
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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 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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Re: [R-sig-phylo] Adding a custom legend underneath a phylo plot with coloured tips
Hi Gabriel. I recommend add.simmap.legend in phytools. For this, though, I would not use par(mfrow) to split the window into multiple plotting devices, but rather xlim or ylim in plotTree (or analogous arguments in plot.phylo) to resize the plot area to accommodate the legend. You should be able to find worked examples on my blog: http://blog.phytools.org/search?q=add.simmap.legend. 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 10/27/2016 11:34 AM, Gabriel Yedid 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 ___ 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/
