Plotting Christmas Tree
🎄 The Tree of Christmas Trees 🎄
I saw a figure of all potential Christmas tree 🎄 at 🐦 Polypompholyx’s Tweet.
It looks strange for my first impression. So I did a quick check from Open Tree. This looks much better!
See code below:
rm(list=ls()) # install.packages("rotl") # install.packages("ape") #loading libraries library("rotl") #for querying open tree database library("ape") #for tree manipulation #First I preapred a table for those potential **Christmas Trees** with first column is common names,a nd second column is the scientific names # then we read in the table as a query list to the Open Tree query <- read.csv("XsmasTree.csv", header=TRUE, sep=",", stringsAsFactors=FALSE, quote="") # check what our table look like this head(query) # query names and get ottid species <- tnrs_match_names(names = query$Scientific_name_rept.) # check results head(species) # fix fuzzy match on row 16, then updated it new_species<- update(species, row_number=16, new_ott_id = 248313) # checking object head(new_species) species <- new_species species.ottid <- ott_id(species) # extracting the phylogeny summarized in the Open tree tree <- tol_induced_subtree(ott_ids=species$ott_id, label_format = "name") # make it looks good tree <- ladderize(tree) plot.phylo(tree, cex=0.8) # rename the tree tip labels query[] <- "Picea pungens" #remove one extra space query[] <- gsub(pattern="\\s", "_", query[]) new_label <- paste0(tree$tip.label,"(", query[][match(tree$tip.label, query[])], ")") new_tree <- tree new_tree$tip.label <- new_label #png("The Tree of Christams Tree.png") #plot(new_tree, cex=0.7) #dev.off() #write.tree(new_tree, "renamed_Xsmas_tree.tre") #plot a prettier tree plot.phylo(new_tree, edge.color = "dark green", edge.width = 2, tip.color = "red", label.offset = 0.5, main="The Tree of Christmas Tree", col.main="red") mtext("---source from Open Tree", col="dark green", 3)
❄️ 🎅 🌵 🔔 ☃️ 🌲
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