ggrasp.load {ggrasp}

ggrasp.load

Description

ggrasp.load() initializes a class GGRaSP object from a file containing either a tree, a distance matrix or a multi-fasta alignment. The returned object can subsequently be clustered using ggrasp.cluster().

Usage

ggrasp.load(file, file.format, rank.file, offset, tree.method = "complete")

Arguments

file

File containing the tree, matrix or sequence alignment used to initialize the ggrasp object. Required.

file.format

The format the file is in, with tree, fasta and matrix accepted. If not given the program makes a guess.

rank.file

File containing the ranks of genomes in a tab-delineated file with the genome in column 1 and the rank in column 2. The rank is a non-negative number.

offset

Numeric representing a perfect match. Default is 0.

tree.method

The method used to make the tree from a distance matrix. "Complete" (Default), "Average", "Single", and "nj" (Neighbor Joining) are currently available.

Value

Returns a class GGRaSP variable

Examples

#The following data is from Chavda et al 2016 which phylotyped Enterobacter genomes
# Our example uses the data underpinning the tree shown in Figure 2
# Also included is a ranking file to prioritize closed Enterobactor genomes

library(ggrasp);
tree.file <- system.file("extdata", "Enter.kSNP.tree", package="ggrasp")
rank.file.in <- system.file("extdata", "Enter.kSNP.ranks", package="ggrasp")
Enter.tree <- ggrasp.load(tree.file, file.format = "tree", rank.file = rank.file.in);

# Other options include loading by fasta file:
fasta.file <- system.file("extdata", "Enter.kSNP2.fasta", package="ggrasp")
rank.file.in <- system.file("extdata", "Enter.kSNP.ranks", package="ggrasp")
Enter.tree <- ggrasp.load(fasta.file, file.format = "fasta", rank.file =rank.file.in)

# and by distance matrix. Since this distance matrix is actually percent identity,
# we will us an offset of 100
mat.file <- system.file("extdata", "Enter.ANI.mat", package="ggrasp")
rank.file.in <- system.file("extdata", "Enter.kSNP.ranks", package="ggrasp")
Enter.in <- ggrasp.load(mat.file, file.format = "matrix", rank.file =rank.file.in, offset = 100)

# Use summary() to examine the data loaded
summary(Enter.in)

#Use plot() to see the tree
plot(Enter.in)