print.ggrasp | R Documentation |
prints formatted information from a class GGRaSP object. Multiple output options are available.
## S3 method for class 'ggrasp'
print(x, type, rank.level, ...)
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 |
#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"));
\donttest{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
\donttest{print(Enter.tree.cluster)}
#Below are examples of using different output formats and rank levels
\donttest{print(Enter.tree.cluster, "tree")}
\donttest{print(Enter.tree.cluster, "table", 1)}
\donttest{print(Enter.tree.cluster, "table", 0)}
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