barplotMulticf: Summarize 'cladeFilter' Result in Barplot
In Chien-Hsun/rePhylo: Re-investigating and Improving Phylogenies

Description Usage Arguments See Also Examples

An internal function of summarizeMulticf to produce summary barplots.

barplotMulticf(
  x,
  type = c("groupings", "genetrees", "species"),
  reorder = "up",
  plot = TRUE,
  pdf = FALSE,
  pwd = c(7, 10, 10)
)

`x`	an object from "`summarizeMulticf`".
`type`	c("`groupings`", "`genetrees`" or "`species`"), specifying the type of the barplots. Defaults to all.
`reorder`	one of "`up`", "`down`" or "`none`", specifying whether to reorder the barplots. Defaults to "`up`".
`plot`	a logical specifying whether to plot barplots. Defaults to `TRUE`.
`pdf`	a logical specifying whether to export plots into pdf files. Defaults to `FALSE`.
`pwd`	Numeric specifying the width of pdf files. Should be in the same length of "`type`". Defaults to c(7,10,10).

summarizeMulticf

data(Brassidata)
trees <- Brassidata$trees
taxa <- Brassidata$taxaTable
# perform cladeFilter analysis
ures <- cladeFilter(trees = trees, taxa = taxa, level = 2)
# summarize cladeFilter results with multiple groupings
usum <- summarizeMulticf(ures, trees, plot.tree = FALSE, write.table = FALSE)
# returns NULL when the grouping covers the whole tree
if(!is.null(usum)){
# to make barplots
utest <- barplotMulticf(x = usum, reorder="up", plot = TRUE, pdf=FALSE)
}