Could not find function
If you got this error, please make sure you are using the latest R and
Packages in Bioconductor, like
ggtree, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to
Sometimes I may write blog post to introduce new functions which is not available in
release branch, you need to install the
devel version of
ggtree in order to use these new functions.
You can download the
devel version of
ggtree from http://bioconductor.org/packages/devel/bioc/html/ggtree.html and install it, or install the github version of
This also applied to other of my packages, including
ChIPseeker. If you got the
could not find function error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you need to install the devel version.
Text & Label
Tip label truncated
ggplot2 can’t auto adjust xlim based on added text.
library(ggtree) ## example tree from https://support.bioconductor.org/p/72398/ tree<-read.tree(text="(Organism1.006G249400.1:0.03977,(Organism2.022118m:0.01337,(Organism3.J34265.1:0.00284,Organism4.G02633.1:0.00468)0.51:0.0104):0.02469);") ggtree(tree) + geom_tiplab()
This is because the units are in two different spaces (data and pixel). Users can use xlim to allocate more space for tip label.
ggtree(tree) + geom_tiplab() + xlim(0, 0.06)
Modify (tip) labels
This could be easily done via the
%<+% operator to attach the modified version of the labels and than use
geom_tiplab to display the modified version.
raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="ggtree") raxml <- read.raxml(raxml_file) lb = get.tree(raxml)$tip.label d = data.frame(label=lb, label2 = paste("AA", substring(lb, 1, 5))) ggtree(raxml) %<+% d + geom_tiplab(aes(label=label2))
Formatting (tip) labels
If you want to format labels, you need to set
geom_tiplab and the
label should be string that can be parsed into expression and displayed as described in
For example, the tiplabels contains two parts, species name and accession number and we want to display species name in italic, we can use command like this:
ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic("species name"), "accession number")', parse=T)
Another example for formating all tip labels:
ggtree(rtree(30)) + geom_tiplab(aes(label=paste0('bold(', label, ')~italic(', node, ')')), parse=TRUE)
label can be provided by a
data.frame that contains related information of the taxa.
tr <- read.tree(text = "((a,(b,c)),d);") genus <- c("Gorilla", "Pan", "Homo", "Pongo") species <- c("gorilla", "spp.", "sapiens", "pygmaeus") geo <- c("Africa", "Africa", "World", "Asia") d <- data.frame(label = tr$tip.label, genus = genus, species = species, geo = geo) ggtree(tr) %<+% d + xlim(NA, 5) + geom_tiplab(aes(label=paste0('italic(', genus, ')~bolditalic(', species, ')~', geo)), parse=T)
Avoid overlapping text labels
User can use ggrepel package to repel overlapping text labels.
library(ggrepel) library(ggtree) raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="ggtree") raxml <- read.raxml(raxml_file) ggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))
For details, please refer to ggrepel usage examples.
bootstrap values from newick format
It’s quite command to store
bootstrap value as node label in
newick format. Visualizing node label is easy using
geom_text2(aes(subset = !isTip, label=label)).
If you want to only display a subset of
bootstrap (e.g. bootstrap > 80), you can’t simply using
geom_text2(subset= (label > 80), label=label) since
label is a character vector, which contains node label (bootstrap value) and tip label (taxa name). If we use
geom_text2(subset=(as.numeric(label) > 80), label=label), it will also fail since
NAs were introduced by coercion. We need to convert
NAs to logical
FALSE, this can be done by the following code:
nwk <- system.file("extdata/RAxML","RAxML_bipartitions.H3", package='ggtree') tr <- read.tree(nwk) ggtree(tr) + geom_text2(aes(label=label, subset = !is.na(as.numeric(label)) & as.numeric(label) > 80))
Another solution is converting the bootstrap value outside
ggtree as I recommended in google group.
q <- ggtree(tr) d <- q$data d <- d[!d$isTip,] d$label <- as.numeric(d$label) d <- d[d$label > 80,] q + geom_text(data=d, aes(label=label))
ggtree(rtree(30)) + geom_point()
For example, we can add symbolic points to nodes with
geom_point() directly. The magic here is we don’t need to map
y position of the points by providing
aes(x, y) to
geom_point() since it was already mapped by
ggtree function and it serves as a global mapping for all layers.
But what if we provide a
dataset in a layer and the
dataset doesn’t contain column of
y, the layer function also try to map
y and also others if you map them in
ggtree function. As these variable is not available in your
dataset, you will get the following error:
Error in eval(expr, envir, enclos) : object 'x' not found
This can be fixed by using parameter
inherit.aes=FALSE which will disable inheriting mapping from
$ in aes
NEVER DO THIS.
see the explaination in the ggplot2 book 2ed:
Never refer to a variable with
aes(). This breaks containment, so that the plot no longer contains everything it needs, and causes problems if ggplot2 changes the order of the rows, as it does when facetting.
colouring edges by user data
see my blog post: Edge coloring with user data and also my answer on https://github.com/GuangchuangYu/ggtree/issues/76 and https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8.