Plot hagis Complexities Objects — autoplot.hagis.complexities • hagis

Creates a ggplot2 object of the frequency of complexity (percent per complexity) or a ggplot2 object of the distribution (number per complexity) calculated by calculate_complexities().

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

Arguments

object: a hagis complexities object generated by calculate_complexities(). Character.
type: a vector of values for which the bar plot is desired. Specify whether to return a graph of the frequency of complexities as a percentage, "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 frequency. Accepts ascending or descending input values. Defaults to complexity value. Character.
...: passed to the chosen geom(s)

Value

A ggplot2 object

Examples

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

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

# Visualize the distribution (count or actual values)
autoplot(complexities, type = "count")

# Visualize the frequency (percentages)
autoplot(complexities, type = "percentage")
}