create_binary_matrix {hagis}

Create Binary Data Matrix From Pathotype Data

Description

Creates a binary data matrix from pathotype data representing the pathotype of each isolate. This binary data matrix can be used to visualize beta-diversity of pathotypes using vegan and ape.

Usage

create_binary_matrix(x, cutoff, control, sample, gene, perc_susc)

Arguments

x

a data.frame containing the data.

cutoff

value for percent susceptible cutoff. Numeric.

control

value used to denote the susceptible control in the gene column. Character.

sample

column providing the unique identification for each sample being tested. Character.

gene

column providing the gene(s) being tested. Character.

perc_susc

column providing the percent susceptible reactions. Character.

Value

a binary matrix of pathotype data

Examples

# Using the built-in data set, `P_sojae_survey`
data(P_sojae_survey)

P_sojae_survey

# calculate susceptibilities with a 60 % cutoff value
final_matrix <- create_binary_matrix(x = P_sojae_survey,
                                    cutoff = 60,
                                    control = "susceptible",
                                    sample = "Isolate",
                                    gene = "Rps",
                                    perc_susc = "perc.susc")
final_matrix