Could not find function

If you got this error, please make sure you are using the latest R and ggtree.

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 devel branch.

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 ggtree.

This also applied to other of my packages, including GOSemSim, DOSE, clusterProfiler, ReactomePA and 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.

## example tree from https://support.bioconductor.org/p/72398/
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))

see also 1 and 2.

Formatting (tip) labels

If you want to format labels, you need to set parse=TRUE in geom_text/geom_tiplab and the label should be string that can be parsed into expression and displayed as described in ?plotmath.

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)

The 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)

see also https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM.

Avoid overlapping text labels

User can use ggrepel package to repel overlapping text labels.

For example:

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))

Here is another exammple for multiple bootstrap support values.

aesthetic mapping

inherit aes

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 x and 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 x and/or y, the layer function also try to map x and 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 ggtree function.

use $ in aes


see the explaination in the ggplot2 book 2ed:

Never refer to a variable with $ (e.g., diamonds$carat) in 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.

see also 1 and 2.