CommT.viz: Visualize tree distances and ANOVA results

In michaelgruenstaeudl/CommT_Code: Comparative Phylogeographic Analysis using the Community Tree Framework

Description

Function to generate a visualization of both the tree distances and ANOVA results.

Usage

CommT.viz(in_df, title_str="a_project_name_here", alpha=0.05, legend_text, legend_pos)

Arguments

in_df	a dataframe storing the tree distances inferred via function CommT.kfdist(). This dataframe constitutes a stacked list of distances grouped by genetic locus and is the default output of function CommT.kfdist()
title_str	a string specifying a title for the resulting plot. The default is a_project_name_here.
alpha	a float specifying the alpha-level employed in the ANOVA. The default is 0.05.
legend_text	a list specifying the ANOVA results to plotted. It constitutes the default output of function CommT.anova()
legend_pos	a list specifying the plot position. It constitutes the default output of function CommT.legendpos()

Author(s)

Michael Gruenstaeudl

Maintainer: Michael Gruenstaeudl [e-mail]

Examples

  # Load libraries
  #  require(ape)

  # Load input data
    data(post_gt_distrs_BEAST)
    data(post_gt_distrs_starBEAST)

  # Calculate KF distances
    in_data = CommT.kfdist(post_gt_distrs_BEAST, post_gt_distrs_starBEAST)

  # Generate ANOVA legend
    legend_text = CommT.anova(in_data)

  # Generate coordinates for plot
    legend_pos = CommT.legendpos(in_data)

  # Visualize KF distances
    my_plot = CommT.viz(in_data, "my_project", alpha=0.05, legend_text, legend_pos)

michaelgruenstaeudl/CommT_Code documentation built on May 22, 2019, 9:50 p.m.