ggrasp.write {ggrasp}

ggrasp.write

Description

writes formatted information from a class GGRaSP object to a file. Multiple output options are available.

Usage

ggrasp.write(x, file, type, rank.level)

Arguments

x

ggrasp-class object to be written

file

String pointing to file where the data will be saved. If no file is given, the result will be printed out on the screen.

type

Format of the data printed, either "tree" (New Hampshire extended style), "table" where the medoids or representative are shown in a table format, "list" where the information is shown in a pseudo-fasta format, or "itol" which prints out a file that can be loaded into the itol phylogeny viewer (http://itol.embl.de) which will color the clades of the different clusters

rank.level

Maximum level of the rank to show. Ignored pre-clustering. After clustering, 0 will show only the medoids, -1 will show all values independent of rank, and any value >= 1 will show all the genomes less than or equal to that rank (including medoids). Default is 0 (only the medoids)

Examples

#Getting the ggrasp object
Enter.tree <- ggrasp.load(system.file("extdata", "Enter.kSNP.tree", package="ggrasp"), 
file.format = "tree", rank.file =system.file("extdata", "Enter.kSNP.ranks", package="ggrasp"));
Enter.tree.cluster <- ggrasp.cluster(Enter.tree)

#Default examples: using the initizalized ggrasp object will 
#write the newick tree string to "tree.nwk"
ggrasp.write(Enter.tree, type="tree", file=file.path(tempdir(), "tree.nwk"));

# Using the clustered ggrasp object will write a text file with the clusters saved as an ITOL clade
# In conjecture with the phylogeny, this is readable by 
# ITOL web phylogeny visualizer (http://itol.embl.de/) 
ggrasp.write(Enter.tree.cluster, type="itol", file=file.path(tempdir(), "tree.itol.clade.txt"));