summarizeMulticf: Summarize 'cladeFilter' Results with Multiple Groupings
In Chien-Hsun/rePhylo: Re-investigating and Improving Phylogenies

Description Usage Arguments See Also Examples

This function summarizes the scenarios of all the groupings for each of the trees, and generates barplots showing the numbers of removing sequences by species (datasets), genetrees (genes) and groupings into pdf files.

summarizeMulticf(
  x,
  trees,
  plot.tree = TRUE,
  write.table = TRUE,
  rm.col = c(rmOnce = "red", rmMulti = "blue"),
  ...
)

`x`	an object from "`cladeFilter`".
`trees`	a list of objects of class "`phylo`". A list of test trees such as single gene trees.
`plot.tree`	a logical specifying whether to plot `trees` with coloring tips to show tips suggested to be removed by `cladeFilter` for all groupings. Defaults to `TRUE`.
`write.table`	a logical specifying whether to write out text files containing the summarized number and names of sequences suggested to be removed by `cladeFilter` for all groupings. Defaults to `TRUE`.
`rm.col`	a character vector specifying the colors for tips removing by one grouping (defalts to `red`) or by multiple groupings (defaults to `blue`).
`...`	other arguments to be passed to `plot` or to `plot.phylo`.

cladeFilter, barplotMulticf

## Not run: 
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)
# to make barplots
utest <- barplotMulticf(x = usum, reorder="up", plot = TRUE, pdf=FALSE)

## End(Not run)