Save a Phylogenetic Tree Object

Create a phylogenetic tree PDF using a phylo tree object and a specimen dataframe.

Usage

savePhytree(
  phyloTree,
  specimen_dataframe,
  tree_file_name = "Phylogenetic Tree.pdf",
  open_PDF = T,
  label_offset = 5.5e-05,
  label_size = 0.3
)

Arguments

phyloTree

A phylo tree object

specimen_dataframe

A specimen dataframe.

tree_file_name

An optional character string to name the PDF file.

open_PDF

A logical value to state whether to open the PDF file.

label_offset

A numerical value to state the label offset distance.

Value

A PDF file.

Examples

# create and plot a phylo tree
specdf_Anth <- querySpecData("Antheraea polyphemus")[1:10,]

DNABin_Anth <- genDNABin(specdf_Anth)

DNAStringset_Anth <- genDNAStringSet(DNABin_Anth)

DNAStringSet_Anth_manipulated <- ManipStringSet(DNAStringset_Anth)
#> ========================================================================================================================================================================================================
#> 
#> Time difference of 0.01 secs
#> Determining distance matrix based on shared 9-mers:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Clustering into groups by similarity:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Aligning Sequences:
#> ================================================================================
#> 
#> Time difference of 0.03 secs
#> 
#> Iteration 1 of 2:
#> 
#> Determining distance matrix based on alignment:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Reclustering into groups by similarity:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Realigning Sequences:
#> ================================================================================
#> 
#> Time difference of 0.04 secs
#> 
#> Alignment converged - skipping remaining iteration.
#> 

Phytree_Anth <- genPhytree(DNAStringSet_Anth_manipulated)

savePhytree(Phytree_Anth, specdf_Anth, "Anth_phylo_tree", 0.000055)