epi_plot_box: Boxplot wrapper function using ggplot2

In AntonioJBT/episcout: Quickly Clean, Explore and Visualise Large Epidemiological Datasets

Boxplot wrapper function using ggplot2

Description

epi_plot_box() wraps ggplot2 boxplot for one or two variables with a number of set preferences, see below.

Usage

epi_plot_box(
  df = NULL,
  var_y = NULL,
  var_x = "",
  outlier_alpha = 0.7,
  fill = "grey80",
  colour = "grey20",
  stat_geom = "errorbar",
  stat_width = 0.5,
  jitter_shape = 16,
  jitter_position = 0.2,
  jitter_alpha = 0.5,
  sum_fun = mean,
  sum_geom = "point",
  sum_shape = 23,
  sum_size = 4,
  ...
)

Arguments

df	data.frame with x var to plot
var_y	Variable to plot on y-axis, pass as a string.
var_x	Variable to plot on x-axis, pass as a string.
outlier_alpha	Outlier transparency. Default is 0.7.
fill	Interior colour used to fill. If only passing var_y it defaults to 'grey80'. If passing both var_y and var_x, it uses var_x.
colour	Aesthetics for ggplot2. Default is 'grey20' if only var_y.
stat_geom	ggplot2::stat_boxplot parameter used for 2 variable boxplot only. Default is 'errorbar'.
stat_width	ggplot2::stat_boxplot parameter used for 2 variable boxplot only. Default is 0.5.
jitter_shape	ggplot2::geom_jitter parameter used for 2 variable boxplot only. Default is 16.
jitter_position	ggplot2::geom_jitter parameter used for 2 variable boxplot only. Default is 0.2.
jitter_alpha	ggplot2::geom_jitter parameter used for 2 variable boxplot only. Default is 0.5.
sum_fun	ggplot2::stat_summary parameter used for 2 variable boxplot only. Default is mean.
sum_geom	ggplot2::stat_summary parameter used for 2 variable boxplot only. Default is "point".
sum_shape	ggplot2::stat_summary parameter used for 2 variable boxplot only. Default is 23.
sum_size	ggplot2::stat_summary parameter used for 2 variable boxplot only. Default is 4.
...	passes any further arguments to ggplot2::geom_boxplot() for both one and two column plots.

Value

Prints a ggplot2 boxplot

Note

For other options, save as object and build on the layers. var_x and var_y are passed to ggplot2::aes. For colour and fill see ggplot2::fill for further information.

Author(s)

Antonio Berlanga-Taylor <\url{https://github.com/AntonioJBT/episcout}>

See Also

epi_plot_list, epi_plots_to_grid, epi_plot_hist, ggplot, geom_boxplot.

Examples

## Not run: 
Boxplot of one variable:
library(ggplot2)
library(ggthemes)
set.seed(12345)
n <- 20
df <- data.frame(var_id = rep(1:(n / 2), each = 2),
                 var_to_rep = rep(c("Pre", "Post"), n / 2),
                 x = rnorm(n),
                 y = rbinom(n, 1, 0.50),
                 z = rpois(n, 2)
                 )
df
df$x # continuous variable
epi_plot_box(df, var_y = 'x')
# Add notch:
epi_plot_box(df, var_y = 'x', notch = TRUE)

# Boxplot for x and y variables:
df$x # continuous variable
df$var_to_rep # factor
epi_plot_box(df, var_x = 'var_to_rep', var_y = 'x')
# Change colours, remove legend, etc.:
my_boxplot <- epi_plot_box(df, var_x = 'var_to_rep', var_y = 'x')
my_boxplot +
  # scale_fill_grey() +
scale_fill_brewer(palette = "Blues") +
  # scale_fill_brewer(palette = "Dark2") +
  theme(legend.position = "none") # Remove legend
# dev.off()

## End(Not run)

AntonioJBT/episcout documentation built on Dec. 1, 2024, 4:07 a.m.