plot.filterCFAZ: plot.filterCFAZ

In chutter/FilterZone: R Package For Detecting the Anomaly Zone and Alignment Filtering in Large Phylogenomic Datasets

Description

Function for plotting data from concordance factors and the anomaly zone

Usage

## S3 method for class 'filterCFAZ'
plot(
  anomaly.zone.data = NULL,
  concordance.factors.data = NULL,
  save.plots = TRUE,
  output.dir = "Filter-Plots",
  focal.node = NULL,
  filter.name = c("alignment_length", "count_pis", "proportion_pis",
    "proportion_sample"),
  dataset.name = "all",
  plot.gcf = TRUE,
  plot.scf = TRUE,
  az.colors = c("#7BC143", "#DE3293"),
  m.shape = c(22, 21),
  min.trees = 10
)

Arguments

anomaly.zone.data	table output from the filterAnomalies function
concordance.factors.data	table output from the filterConcordance function
save.plots	if you wish to save to file select TRUE
output.dir	the name of the output directory to save the plots if TRUE above
focal.node	the node annotated from the filterConcordance function
filter.name	the filter to plot. Options include: alignment_length, count_pis, proportion_pis, proportion_sample
dataset.name	from your main sets of data (i.e. exons, introns). All = plots of all them.
plot.gcf	should the gene concordance factor be plotted?
plot.scf	should the site concordance factor be plotted?
az.colors	colors to indicate the anomaly zone. Default: Green: presence; Purple: absence
m.shape	monophyly shape on the graph; circle = monophyletic; square paraphyletic
min.trees	minimum number of trees to keep a filtration replicate. Default: 10

Value

plots a dot plot of each filter and the concordance factors for the focal node. Monophyly of that node is also shown.

Examples

your.tree = ape::read.tree(file = "file-path-to-tree.tre")
astral.data = astralPlane(astral.tree = your.tree,
                          outgroups = c("species_one", "species_two"),
                          tip.length = 1)

chutter/FilterZone documentation built on Dec. 19, 2021, 4:07 p.m.