print.ggrasp {ggrasp}

print.ggrasp

Description

prints formatted information from a class GGRaSP object. Multiple output options are available.

Usage

## S3 method for class 'ggrasp'
print(x, type, rank.level, ...)

Arguments

x

ggrasp-class object to be printed

type

Format of the data printed, either "tree" (new hampshire extended style), "table" where the medoids or representative are shown in a table format, or "list" where the information is shown in a pseudo-fasta format

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)

...

ignored

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 print the newick tree string 
print(Enter.tree);

# Using the clustered ggrasp object will print the medoids and their respective clusters
print(Enter.tree.cluster)
#Below are examples of using different output formats and rank levels
print(Enter.tree.cluster, "tree")
print(Enter.tree.cluster, "table", 1)
print(Enter.tree.cluster, "table", 0)