generate_tree_vis: Combine trees and phylogenetic matrix data as a ggplot object
In wrightaprilm/treesiftr: Visualizing The Relationship Between Phylogeny and Data

Description Usage Arguments Value Examples

View source: R/generate_tree_vis.R

This function calls generate_tree_vec() to generate a vector of phylogenetic trees under parsimony. It then plots them alongside the phylogenetic matrix that was used to estimate the tree. Optional decorations can be added displaying parsimony and likelihood scores.

1 2	generate_tree_vis(sample_df, alignment, tree, phy_mat, pscore = FALSE, lscore = FALSE, random_tree = FALSE)

`sample_df`	Dataframe specifying how to subsample phylogenetic matrix
`alignment`	String specifying path to alignment
`tree`	Starting tree for parsimony analysis. Phylo object.
`phy_mat`	Phylogenetic matrix to be subsampled
`pscore`	Optional boolean specifying if you would like figures annotated with parsimony score of tree given data. Default FALSE.
`lscore`	Optional boolean specifying if you would like figures annotated with likelihood score of tree given data under the Mk model. Default FALSE.
`random_tree`	Optional boolean specifying if you would like to view a vector of random trees

vector Vector of ggplot2 objects

## Not run: 
output_vector <- generate_tree_vis(sample_df = sample_df,
                                   alignment = aln_path, tree = tree,
                                   phy_mat = bears, pscore = TRUE,
                                   lscore = TRUE)

## End(Not run)