Package index • hagis

Calculations

Fetch and read the AAGIS regions

calculate_complexities(): Calculate Distribution of Complexities by Sample

calculate_diversities(): Calculate Diversities Indices

summarize_gene(): Calculate and Summarize Distribution of Susceptibilities by Gene

Data

Example data included in {hagis}

P_sojae_survey: Phytophthora sojae Survey Example Data

sample_meta: Phytophthora sojae Survey Example Metadata

Miscellaneous

Helper functions for using {hagis}

create_binary_matrix(): Create Binary Data Matrix From Pathotype Data

Plotting

Visualise {hagis} outputs with ggplot2::autoplot()

autoplot(<hagis.complexities>): Plot hagis Complexities Objects

autoplot(<hagis.gene.summary>): Plot hagis Summary Objects

Printing

Custom print methods for {hagis} objects in your R session

diversities_table(): Custom Print for hagis Diversities Tables

individual_pathotypes(): Prints Individual Pathotypes for Each Sample