walkthrough.R

Visualizing character data on trees

library(ape)
library(diversitree)

## Loading required package: deSolve
## Loading required package: subplex
## Loading required package: Rcpp

source('/Users/alex/GitHub/traitathon/treeOfSex/plot_trait_dendrogram.R')
source('/Users/alex/GitHub/traitathon/treeOfSex/get_tos_database.R')

Example 1: Plotting binary flower color character states onto Solanaceae data

Here we already have a tree and a character matrix
First, read in the tree with ape() and the character matrix, too.

sol_tree <- read.tree("/Users/alex/GitHub/traitathon/solanaceae/Solanaceae.tre")
sol_char <- read.csv("/Users/alex/GitHub/traitathon/solanaceae/SolanaceaeTraits.csv", row.names=1)

Then make sure the character matrix rows are in the same order as the tree tips. This is essential, otherwise they won’t match up on the tree.

sol_char <- sol_char[sol_tree$tip.label, ]

We only have one binary character that we want to map onto the tree, so we can plot that single column.

plot_trait_dendrogram(sol_tree, sol_char, legend=TRUE, binary=TRUE, tree_type="fan", tiplabel_cex=0.2)

Example 2: Visualizing discrete traits from Anolis

Again, here we have a user-provided tree and character matrix

anolis_tree <- read.tree("/Users/alex/GitHub/traitathon/anolis/anolis.phy") 
anolis_char <- read.csv("/Users/alex/GitHub/traitathon/anolis/anolis.csv", row.names=1)

Make sure the character matrix rows are in the same order as the tree tips

anolis_char <- anolis_char[anolis_tree$tip.label, ]

Pick out the character trait to plot on the tree. Here I extract what islands each species is native to.

anolis_char <- anolis_char$island

plot_trait_dendrogram(anolis_tree, anolis_char, legend=TRUE, binary=FALSE, tree_type="fan", tiplabel_cex=0.5)

Maybe this would look better as a regular phylogram…

plot_trait_dendrogram(anolis_tree, anolis_char, legend=TRUE, binary=FALSE, tree_type="phylogram", tiplabel_cex=0.25)

Example 3: Visualizing discrete and continuous floral traits on a Heliconia tree

helic_tree <- read.tree("/Users/alex/GitHub/traitathon/heliconia/heliconia.phy")
helic_char <- read.csv("/Users/alex/GitHub/traitathon/heliconia/heliconia1.csv", row.names=1)

Again, let’s make sure the rownames of the character matrix match up with the tree tips

helic_char <- helic_char[helic_tree$tip.label, ]

Let’s pick out a character trait to plot, like flower arrangement, or perianth color

helic_arrangement <- helic_char$arrangment
helic_color <- helic_char$perColor

Now plot it

plot_trait_dendrogram(helic_tree, helic_arrangement, legend=TRUE, binary=FALSE, tree_type="phylogram", tiplabel_cex=0.4, legend_loc="bottomleft")

Example 4: Attach other sources of data to a tree (Tree of Sex)

Let’s say we have a tree, but want to extract some other types of character data. For instance, I’d like to use the Tree of Sex database to see if there’s any hermaphroditism in my group.
Using the heliconia tree from the previous example, let’s map some other characteristics onto it.

First let’s extract some data from the Tree of Sex
# rename

plant_sex <- get_tos_database("plant")

## loading plant db

What traits are in this database?

colnames(plant_sex)

##  [1] "kingdom"                "higher_taxonomic_group"
##  [3] "order"                  "family"                
##  [5] "genus"                  "species"               
##  [7] "species_author"         "infraspecific"         
##  [9] "common_name"            "hybrid"                
## [11] "hybrid_source"          "plant_list_status"     
## [13] "plant_list_name"        "sexual_system"         
## [15] "sexual_system_source"   "selfing"               
## [17] "selfing_source"         "growth_form"           
## [19] "growth_form_source"     "woodiness"             
## [21] "woodiness_count"        "woodiness_source"      
## [23] "life_form"              "life_form_source"      
## [25] "gametophytic_n"         "gametophytic_n_min"    
## [27] "gametophytic_n_mean"    "gametophytic_n_source" 
## [29] "sporophytic_n"          "sporophytic_n_min"     
## [31] "sporophytic_n_mean"     "sporophytic_n_source"  
## [33] "karyotype"              "karyotype_source"      
## [35] "molecular_basis"        "molecular_basis_source"
## [37] "genotype"               "genotype_source"       
## [39] "notes"                  "entry_email"

Let’s reformat this data a little bit. We want the rownames to be “Genus species”.

new_rownames <- paste(plant_sex$genus,plant_sex$species, sep=" ")
rownames(plant_sex) <- make.names(new_rownames, unique=TRUE)
rownames(plant_sex) <- as.character(sub("\\."," ", rownames(plant_sex)))
head(rownames(plant_sex))

## [1] "Acer acuminatum"                     
## [2] "Acer albopurpurascens"               
## [3] "Acer albopurpurascens...buergerianum"
## [4] "Acer amamiense"                      
## [5] "Acer amplum"                         
## [6] "Acer argutum"

Now we can extract some information…like sexual systems in the solanaceae example
The tree tip labels in the solanacea have underscores in them, let’s change that real quick to match our Tree of Sex data

head(sol_tree$tip.label)

## [1] "Vestia_foetida"          "Protoschwenkia_mandonii"
## [3] "Browallia_americana"     "Browallia_eludens"      
## [5] "Browallia_speciosa"      "Streptosolen_jamesonii"

sol_tree$tip.label <- sub("_"," ",sol_tree$tip.label)
head(sol_tree$tip.label)

## [1] "Vestia foetida"          "Protoschwenkia mandonii"
## [3] "Browallia americana"     "Browallia eludens"      
## [5] "Browallia speciosa"      "Streptosolen jamesonii"

Now extract the Tree of Sex “sexual system” data for leaves in our tree. If there’s no entry for a tip species in the Tree of Sex database, title it “unknown”

tipchars <- ifelse(sol_tree$tip.label %in% rownames(plant_sex),plant_sex$sexual_system,NA)
sex_levels <- levels(plant_sex$sexual_system)
solanacea_sex <- sex_levels[tipchars]
solanacea_sex[is.na(solanacea_sex)] <- "unknown" 
solanacea_sex <- as.factor(solanacea_sex)

let’s see if it worked…!

plot_trait_dendrogram(sol_tree, solanacea_sex, tree_type="fan", tiplabel_cex=0.15, legend=TRUE, legend_loc="bottomleft", legend_cex=0.6)

Whoops. There are two conditions colored black; we need more colors in our color palette. Here’s how we could fix that

palette(c("blue","red", "yellow","orange","purple","black","green","lightblue","grey"))
plot_trait_dendrogram(sol_tree, solanacea_sex, tree_type="fan", tiplabel_cex=0.15, legend=TRUE, legend_loc="bottomleft", legend_cex=0.6)