In McTavishLab/physcraperex: Physcraper Workflow Examples

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
knitr::opts_knit$set(
  global.par = TRUE
  )
options(rmarkdown.html_vignette.check_title = FALSE)

library(DT)

I. Finding a tree to update

With the Open Tree of Life website

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

Oh no... it seems like the Dothideomycetes are not represented as a clade on the Open Tree of Life synthetic tree (at the middle of year 2020):

knitr::include_graphics("dothideomycetes-tree-opentree-2020-06-06.png")

---

What is the MRCA of the "broken" Dothideomycetes in the synthetic tree? follow the "View the MRCA of the members of this taxon in the synthetic tree" link.

knitr::include_graphics("ascomycota-tree-opentree-2020-06-06.png")

It is the Ascomycota, which has more than 1.5k species.

It is time now to ask the question, do we want to update an alignment for all the Ascomycota???

---

Why are the Dothideomycetes "broken"?

go to the "Show this tree's conflicts in the study curation tool" link.

knitr::include_graphics("dothideomycetes-conflict-opentree-2020-06-06.png")

There is a published tree that is conflicting with the taxonomy.

---

Let's get more information about the taxonomy of the Dothideomycetes, follow the "View this taxon in the taxonomy browser" link.

knitr::include_graphics("dothideomycetes-taxonomy-opentree-2020-06-06.png")

So, it seems like it is a taxon in NCBI. To verify this, go to the section "Taxon details", and follow the ncbi:147541 link.

knitr::include_graphics("dothideomycetes-ncbi-2020-06-06.png")

Maybe we can just enrich that part of the tree on the updating step.

---

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

Studies matching the word 'dothideomycetes' on the curator database, at the middle of year 2020. Some of these studies are not actually about this taxon.

knitr::include_graphics(c("dothideomycetes-curation-opentree-1-2020-06-06.png", "dothideomycetes-curation-opentree-2-2020-06-06.png", "dothideomycetes-curation-opentree-3-2020-06-06.png"))

Finding a tree to update 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.

doth <- rotl::studies_find_studies(property="ot:focalCladeOTTTaxonName", value="Dothideomycetes")

# knitr::kable(doth, caption = "Studies with the class **Dothideomycetes** as focal clade.")
issue_title <- doth[,"study_ids"] %in% "ot_465"
doth[issue_title, "title"] <- "Resolving Tiarosporella spp. allied to Botryosphaeriaceae and Phacidiaceae"
datatable(doth, class = 'order-column hover compact row-border', options = list(dom = 't'), rownames = FALSE, editable = FALSE) # %>%

It seems like the tree tree137 from study pg_254, is not 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

schoch2009 <- rotl::get_study_tree(study_id = "pg_254", tree_id = "tree137")
ape::plot.phylo(ape::ladderize(schoch2009), type = "phylogram", cex = 0.3, label.offset = 1, edge.width = 0.5)

The alignment is here https://treebase.org/treebase-web/search/study/matrices.html?id=10245.

wget "http://purl.org/phylo/treebase/phylows/matrix/TB2:M4727?format=nexus" mv TB2:M4727?format=nexus data-raw/alignments/T6859-M4727.nex

Ascomycota

asco <- rotl::studies_find_studies(property="ot:focalCladeOTTTaxonName", value="Ascomycota")
datatable(asco, class = 'order-column hover compact row-border', options = list(dom = 't'), rownames = FALSE, editable = FALSE)
knitr::kable(asco, caption = "Studies with the **Ascomycota** as focal clade.")

It seems like the tree tree109 from study pg_238, is not in the Open Tree of Life synthetic tree.

Ascomycota alignments here https://treebase.org/treebase-web/search/study/matrices.html?id=2137.

wget "http://purl.org/phylo/treebase/phylows/matrix/TB2:M3939?format=nexus"
mv TB2:M3939?format=nexus data-raw/alignments/Tr5276-M3939.nex

wget "http://purl.org/phylo/treebase/phylows/matrix/TB2:M3938?format=nexus"
mv TB2:M3938?format=nexus data-raw/alignments/Tr5276-M3938.nex

wget "http://purl.org/phylo/treebase/phylows/matrix/TB2:M3802?format=nexus"
mv TB2:M3802?format=nexus data-raw/alignments/Tr5276-M3802.nex

wget "http://purl.org/phylo/treebase/phylows/matrix/TB2:M3956?format=nexus"
mv TB2:M3956?format=nexus data-raw/alignments/Tr5276-M3956.nex

Downloading them with physcraper

physcraper_run.py -s pg_238 -t tree109 -tb -no_est -o ../physcraperex/data/schoch_ascomycota_0_2020.06.06

Current run

physcraper_run.py -s pg_238 -t tree109 -a ../physcraperex/data-raw/alignments/Tr5276-M3939-mod.nex -as nexus  -db /branchinecta/shared/local_blast_db -o ../physcraperex/data/schoch_ascomycota_1_2020.06.06

McTavishLab/physcraperex documentation built on April 10, 2021, 12:02 a.m.