hagis (version 3.1.12)

autoplot.hagis.complexities: Plot hagis Complexities Objects

Description

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().

Usage

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

Value

A ggplot2 object

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)

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")
}