ggsummarystats: GGPLOT with Summary Stats Table Under the Plot

In ggpubr: 'ggplot2' Based Publication Ready Plots

GGPLOT with Summary Stats Table Under the Plot

Description

Create a ggplot with summary stats (n, median, mean, iqr) table under the plot. Read more: How to Create a Beautiful Plots in R with Summary Statistics Labels.

Usage

ggsummarytable(
  data,
  x,
  y,
  digits = 0,
  size = 3,
  color = "black",
  palette = NULL,
  facet.by = NULL,
  labeller = "label_value",
  position = "identity",
  ggtheme = theme_pubr(),
  ...
)

ggsummarystats(
  data,
  x,
  y,
  summaries = c("n", "median", "iqr"),
  ggfunc = ggboxplot,
  color = "black",
  fill = "white",
  palette = NULL,
  facet.by = NULL,
  free.panels = FALSE,
  labeller = "label_value",
  heights = c(0.8, 0.2),
  digits = 0,
  table.font.size = 3,
  ggtheme = theme_pubr(),
  ...
)

## S3 method for class 'ggsummarystats'
print(x, heights = c(0.8, 0.2), ...)

## S3 method for class 'ggsummarystats_list'
print(x, heights = c(0.8, 0.2), legend = NULL, ...)

Arguments

data	a data frame
x	a list of ggsummarystats.
y	character vector containing one or more variables to plot
digits	integer indicating the number of decimal places (round) to be used.
size	Numeric value (e.g.: size = 1). change the size of points and outlines.
color	outline color.
palette	the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".
facet.by	character vector, of length 1 or 2, specifying grouping variables for faceting the plot into multiple panels. Should be in the data.
labeller	Character vector. An alternative to the argument short.panel.labs. Possible values are one of "label_both" (panel labelled by both grouping variable names and levels) and "label_value" (panel labelled with only grouping levels).
position	Position adjustment, either as a string, or the result of a call to a position adjustment function.
ggtheme	function, ggplot2 theme name. Default value is theme_pubr(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....
...	other arguments passed to the function ggpar(), facet() or ggarrange() when printing the plot.
summaries	summary stats to display in the table. Possible values are those returned by the function get_summary_stats(), including: "n", "min", "max", "median", "q1", "q2", "q3", "mad", "mean", "sd", "se", "ci".
ggfunc	a ggpubr function, including: ggboxplot, ggviolin, ggdotplot, ggbarplot, ggline, etc. Can be any other ggplot function that accepts the following arguments data, x, color, fill, palette, ggtheme, facet.by.
fill	fill color.
free.panels	logical. If TRUE, create free plot panels when the argument facet.by is specified.
heights	a numeric vector of length 2, specifying the heights of the main and the summary table, respectively.
table.font.size	the summary table font size.
legend	character specifying legend position. Allowed values are one of c("top", "bottom", "left", "right", "none"). To remove the legend use legend = "none".

Functions

• ggsummarytable(): Create a table of summary stats

• ggsummarystats(): Create a ggplot with a summary stat table under the plot.

Examples

# Data preparation
#::::::::::::::::::::::::::::::::::::::::::::::::
data("ToothGrowth")
df <- ToothGrowth
df$dose <- as.factor(df$dose)
# Add random QC column
set.seed(123)
qc <- rep(c("pass", "fail"), 30)
df$qc <- as.factor(sample(qc, 60))
# Inspect the data
head(df)


# Basic summary stats
#::::::::::::::::::::::::::::::::::::::::::::::::
# Compute summary statistics
summary.stats <- df %>%
  group_by(dose) %>%
  get_summary_stats(type = "common")
summary.stats

# Visualize summary table
ggsummarytable(
  summary.stats, x = "dose", y = c("n", "median", "iqr"),
  ggtheme = theme_bw()
)


# Create plots with summary table under the plot
#::::::::::::::::::::::::::::::::::::::::::::::::
# Basic plot
ggsummarystats(
  df, x = "dose", y = "len",
  ggfunc = ggboxplot, add = "jitter"
)

# Color by groups
ggsummarystats(
  df, x = "dose", y = "len",
  ggfunc = ggboxplot, add = "jitter",
  color = "dose", palette = "npg"
)

# Create a barplot
ggsummarystats(
  df, x = "dose", y = "len",
  ggfunc = ggbarplot, add = c("jitter", "median_iqr"),
  color = "dose", palette = "npg"
)

# Facet
#::::::::::::::::::::::::::::::::::::::::::::::::
# Specify free.panels = TRUE for free panels
ggsummarystats(
  df, x = "dose", y = "len",
  ggfunc = ggboxplot, add = "jitter",
  color = "dose", palette = "npg",
  facet.by = c("supp", "qc"),
  labeller = "label_both"
)

ggpubr documentation built on Feb. 16, 2023, 7:18 p.m.