In andrew-hipp/edivColl: Evolutionary Diversity of Collections

generate figure for IMLS document

First, get edivColl attached:

  library(edivColl)
  ## and a couple of work-arounds till the package is updated with correct namespace
  library(ggplot2)
  library(magrittr)

Then bring in tree

data(ulmus_tr)
data(accessions.mor) # read MOR accessions data
data(desiderata.mor) # read MOR desiderata list

Now clean data

ulmus2 <- ulmus
ulmus2$tip.label <- paste('Ulmus', ulmus$tip.label)
temp <- 
  c(accessions.mor$Taxon, desiderata.mor$taxon_name) %>%
  unique %>% sort
dat.mor <- 
  data.frame(inGarden = temp %in% accessions.mor$Taxon,
    wanted = temp %in% desiderata.mor$taxon_name,
    row.names = temp)
rm(temp)
combo.ulmus <- make.consInt(ulmus2, dat.mor)

Now do the evolutionary distinctiveness:

ulmus.e <- eDisCalc(combo.ulmus)

pdf('ulmus.e.pdf', 5, 7)
ulmus.p <- 
  edivColl:::plot.eDis(ulmus.e, hWidth = 0.075, hOff = 16, legPos = c(0.2, 0.915))
print(ulmus.p)
dev.off()