ggphylomorpho: Make a phylomorphospace plot

Description Usage Arguments Value

Description

Make a phylomorphospace plot

Usage

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ggphylomorpho(tree, tipinfo, xvar = PC1, yvar = PC2, factorvar = group,
  labelvar = taxon, title = "Phylomorphospace", xlab = "PC1",
  ylab = "PC2", repel = TRUE, edge.width = 1, fontface = "italic",
  tree.alpha = 0.7)

Arguments

tree

object of class phylo

tipinfo

a dataframe containing two continuous variables (typically PC1 and PC2 from a PCA) as well as a grouping variable and a variable of labels for each point on the plot

xvar

the unquoted name of the column containing the x variable in the tipinfo dataframe. Defaults to PC1

yvar

the unquoted name of the column containing the y variable in the tipinfo dataframe. Defaults to PC2

factorvar

the unquoted name of the column containing the grouping variable in the tipinfo dataframe. Defaults to group

labelvar

the unquoted name of the column containing the labeling variable in the tipinfo dataframe. Defaults to taxon

title

the text string to use as the title of the phylomorphospace plot

xlab

the text label for the x axis

ylab

the text label for the y axis

repel

boolean indicating whether or not to use the ggrepel package to prevent overplotting of labels

edge.width

size parameter for edges drawn on phylomorphospace. Default is 1

fontface

font face for labels. Default is "italic".

tree.alpha

alpha parameter for the main tree. default is 0.7

Value

the ggplot object representing the phylomorphospace


wabarr/ggphylomorpho documentation built on May 3, 2019, 2:57 p.m.