In McTavishLab/physcraperex: Physcraper Workflow Examples

screenshot_date <- "May 25, 2020"

Using the Open Tree of Life website

Go to the Open Tree of Life website and use the "search for taxon" menu to look up for the taxon Ilex.

The screenshpt below shows the state of the genus Ilex in the Open Tree of Life synthetic tree on r screenshot_date. If you go to OpenTree's website you can check out Ilex current state here.

# library(webshot)
# webshot("https://tree.opentreeoflife.org/opentree/argus/ottol@727571/Ilex", "ilex-tree-opentree.png", delay = 1)

# webshot works on opentree website if I set up a delay!
knitr::include_graphics("ilex-tree-opentree-2020-05-31.png")

Navigating into the tree, we notice that there might be two studies associated to this portion of the Open Tree synthetic tree.

knitr::include_graphics("ilex-tree-opentree-2020-05-31-2.png")

Let's verify that on the study curator of OToL.

Studies matching the word 'ilex' on the curator database, at the middle of year 2020. Some of these studies are not actually about the hollies, but other taxa that have the species epithet ilex, e.g., the holly oak Quercus ilex or the rodent Apodemus ilex

knitr::include_graphics("ilex-curation-opentree-2020-05-31.png")

Using the R package rotl

Explain what a focal clade is.

There is a handy function that will search a taxon among the focal clades reported across trees.

studies <- rotl::studies_find_studies(property="ot:focalCladeOTTTaxonName", value="Ilex")

knitr::kable(studies, caption = "Studies with the genus *Ilex* as focal clade.")

study2003 <-  studies$study_doi %in% "http://dx.doi.org/10.3732/ajb.92.2.352"

It seems like the oldest tree, r studies$candidate[study2003] from study r studies$study_ids[study2003], is in the Open Tree of Life synthetic tree.

Let's get it and plot it here:

par(mar=c(0,1,0,0), xpd=NA)  # adjust margins for all plots after this

original_tree <- rotl::get_study_tree(study_id = "pg_2827", tree_id = "tree6577")
ape::plot.phylo(ape::ladderize(original_tree), type = "phylogram", cex = 0.3, label.offset = 1, edge.width = 0.5)

Now, let's look at some properties of the tree:

ape::Ntip(original_tree)  # gets the number of tips
ape::is.rooted(original_tree)  # check that it is rooted
ape::is.binary(original_tree)  # check that it is fully resolved
datelife::phylo_has_brlen(original_tree)  # checks that it has branch lengths

The tree has r ape::Ntip(original_tree) tips, is rooted, has no branch lengths and is not fully resolved, as you probably already noted. Also, labels correspond to the labels reported on the original study here. Other labels are available to use as tip labels. For example, you can plot the tree using the unified taxonomic names, or the taxonomic ids.