Plot hagis Summary Objects — autoplot.hagis.gene.summary • hagis

Creates a ggplot2 object of the gene summaries calculated by summarize_gene()

# S3 method for hagis.gene.summary
autoplot(object, type, color = NULL, order = NULL, ...)

Arguments

object: a hagis.gene.summary object generated by summarize_gene(). Character.
type: a vector of values for which the bar plot is desired. Specify whether to return a graph of the percent pathogenic isolates, percentage, or as the count, count. Character.
color: a named or hexadecimal color value to use for the bar color
order: sort the x-axis of the bar chart by ascending or descending order of N_virulent_isolates or percent_pathogenic. Accepts ascending or descending input values. Defaults to gene name. Character.
...: passed to the chosen geom(s)

Value

A ggplot2 plot

Examples

if (FALSE) { # interactive()
# Using the built-in data set, `P_sojae_survey`
data(P_sojae_survey)

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

# Visualize the summary of genes
autoplot(susc, type = "percentage")
}