individual_pathotypes: Prints Individual Pathotypes for Each Sample

In hagis: Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity

Prints Individual Pathotypes for Each Sample

Description

Print an object from a hagis.diversities object with individual pathotypes, i.e. each sample's pathotype. The resulting object is a pander table (a text object for Markdown) for ease of use in reporting and viewing in the console.

Usage

individual_pathotypes(x, ...)

Arguments

x	a hagis.diversities object generated by calculate_diversities()
...	other arguments passed to pander::panderOptions()

Value

A pander object of individual pathotypes

See Also

calculate_diversities(), diversities_table()

Examples

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

P_sojae_survey

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

# print the diversities table
individual_pathotypes(diversities)

hagis documentation built on Sept. 8, 2023, 5:20 p.m.