pubrplot (version 0.0.1)

plot_numeric: Publication-Quality Numeric Plot with Optional Grouping and Statistical Tests

Description

Creates a publication-ready plot for numeric variables, including bar plots, violin plots, boxplots, and combinations (violin + box, violin + jitter, box + jitter). Supports error bars (SD, SE, CI), group comparisons, and automatic or specified statistical tests with optional post-hoc annotations.

Usage

plot_numeric(
  data,
  var,
  by,
  geom_type = c("bar", "violin", "box", "violin_box", "violin_jitter", "box_jitter"),
  error = c("sd", "se", "ci"),
  test.type = c("auto", "parametric", "nonparametric"),
  vjust = 0,
  rotate = FALSE,
  x.lab = "Group",
  y.lab = NULL,
  text.size = 3.5,
  color.violin = NULL,
  color.box = NULL,
  box.color = "black",
  color.jitter = "black",
  jitter.size = 1.5,
  ptext.size = 3,
  theme_fun = ggthemes::theme_stata,
  bar.width = 0.85,
  box.width = 0.2,
  show.posthoc = TRUE,
  err.mult = 1.5,
  position.p = NULL,
  jitter.width = 0.1
)

Value

A ggplot2 object representing the numeric variable plot.

Arguments

data

A data frame containing the variables to plot.

var

Numeric variable to plot (unquoted).

by

Optional grouping variable (unquoted) to create separate groups.

geom_type

Type of plot: "bar", "violin", "box", "violin_box", "violin_jitter", "box_jitter".

error

Type of error to display for bar plots: "sd", "se", or "ci".

test.type

Statistical test type: "auto", "parametric", or "nonparametric".

vjust

Vertical adjustment for text labels. Default is 0.

rotate

Logical, whether to rotate x-axis labels. Default is FALSE.

x.lab

Label for x-axis. Default is "Group".

y.lab

Label for y-axis. Defaults to variable name.

text.size

Size of labels above bars or violin/box plots. Default is 3.5.

color.violin

Fill color for violin plots. Can be a vector of colors per group.

color.box

Fill color for boxplots inside violins. Can be a vector of colors per group.

box.color

Outline color for boxplots. Default is "black".

color.jitter

Color of jittered points. Default is "black".

jitter.size

Size of jittered points. Default is 1.5.

ptext.size

Size of text for post-hoc annotations. Default is 3.

theme_fun

Theme function from ggthemes or ggplot2 for styling. Default is ggthemes::theme_stata.

bar.width

Width of bars for bar plots. Default is 0.85.

box.width

Width of boxplots inside violin. Default is 0.2.

show.posthoc

Logical, whether to display post-hoc test results. Default is TRUE.

err.mult

Multiplier for error bars (SD/SE/CI). Default is 1.5.

position.p

Optional vector c(x, y) to place post-hoc text manually.

jitter.width

Width of jitter for points in violin_jitter or box_jitter plots. Default is 0.1.

Examples

# Violin + Box plot for iris dataset
plot_numeric(
  data = iris,
  var = Sepal.Length,
  by = Species,
  geom_type = "violin_box",
  box.width = 0.1,
  color.violin = c("#377eb8", "#ff7f00", "#4daf4a"),
  color.box = c("darkgreen", "#a65628", "#f781bf"),
  box.color = "black",
  color.jitter = "red",
  position.p = c(1,9),
  jitter.size = 2,
  ptext.size = 4,
  show.posthoc = TRUE
)

# Simple bar plot with error bars
plot_numeric(
  data = iris,
  var = Sepal.Length,
  by = Species,
  geom_type = "bar",
  error = "se"
)

# Violin plot with jitter points
plot_numeric(
  data = iris,
  var = Sepal.Length,
  by = Species,
  geom_type = "violin_jitter"
)