% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ggpaired.R
\name{ggpaired}
\alias{ggpaired}
\title{Plot Paired Data}
\usage{
ggpaired(
  data,
  cond1,
  cond2,
  x = NULL,
  y = NULL,
  id = NULL,
  color = "black",
  fill = "white",
  palette = NULL,
  width = 0.5,
  point.size = 1.2,
  line.size = 0.5,
  line.color = "black",
  linetype = "solid",
  title = NULL,
  xlab = "Condition",
  ylab = "Value",
  facet.by = NULL,
  panel.labs = NULL,
  short.panel.labs = TRUE,
  label = NULL,
  font.label = list(size = 11, color = "black"),
  label.select = NULL,
  repel = FALSE,
  label.rectangle = FALSE,
  ggtheme = theme_pubr(),
  jitter = 0,
  ...
)
}
\arguments{
\item{data}{a data frame}

\item{cond1}{variable name corresponding to the first condition.}

\item{cond2}{variable name corresponding to the second condition.}

\item{x, y}{x and y variables, where x is a grouping variable and y contains
values for each group. Considered only when \code{cond1} and \code{cond2}
are missing.}

\item{id}{variable name corresponding to paired samples' id. Used to connect
paired points with lines.}

\item{color}{points and box plot colors. To color by conditions, use color =
"condition".}

\item{fill}{box plot fill color. To change fill color by conditions, use fill
= "condition".}

\item{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".}

\item{width}{box plot width.}

\item{point.size, line.size}{point and line size, respectively.}

\item{line.color}{line color.}

\item{linetype}{line type.}

\item{title}{plot main title.}

\item{xlab}{character vector specifying x axis labels. Use xlab = FALSE to
hide xlab.}

\item{ylab}{character vector specifying y axis labels. Use ylab = FALSE to
hide ylab.}

\item{facet.by}{character vector, of length 1 or 2, specifying grouping
variables for faceting the plot into multiple panels. Should be in the data.}

\item{panel.labs}{a list of one or two character vectors to modify facet panel
labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies
the labels for the "sex" variable. For two grouping variables, you can use
for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs",
"Lev", "Lev2") ).}

\item{short.panel.labs}{logical value. Default is TRUE. If TRUE, create short
labels for panels by omitting variable names; in other words panels will be
labelled only by variable grouping levels.}

\item{label}{the name of the column containing point labels. Can be also a
character vector with length = nrow(data).}

\item{font.label}{a list which can contain the combination of the following
elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic",
"bold.italic") and the color (e.g.: "red") of labels. For example font.label
= list(size = 14, face = "bold", color ="red"). To specify only the size and
the style, use font.label = list(size = 14, face = "plain").}

\item{label.select}{can be of two formats: \itemize{ \item a character vector
specifying some labels to show. \item a list containing one or the
combination of the following components: \itemize{ \item \code{top.up} and
\code{top.down}: to display the labels  of the top up/down points. For
example, \code{label.select = list(top.up = 10, top.down = 4)}. \item
\code{criteria}: to filter, for example, by x and y variables values, use
this: \code{label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` \%in\%
c('A', 'B')")}. } }}

\item{repel}{a logical value, whether to use ggrepel to avoid overplotting
text labels or not.}

\item{label.rectangle}{logical value. If TRUE, add rectangle underneath the
text, making it easier to read.}

\item{ggtheme}{function, ggplot2 theme name. Default value is theme_pubr(). Set ggtheme = NULL to skip applying a ggpubr theme, so the plot keeps ggplot2 default theme or the theme set globally via theme_set().
Allowed values include ggplot2 official themes: theme_gray(), theme_bw(),
theme_minimal(), theme_classic(), theme_void(), ....}

\item{jitter}{numeric value (default 0, no jitter) giving the amount of
horizontal jitter added to the paired points to reduce overlap. Points are
nudged sideways within \code{[-jitter, jitter]}; each subject (\code{id})
gets a single offset so its two points move together and the connecting
line stays intact. Only the horizontal positions change (the values are
never moved). Typical values are small relative to the box \code{width}
(e.g. \code{jitter = 0.05} to \code{0.1}). \code{jitter = 0} leaves the plot
unchanged.}

\item{...}{other arguments to be passed to be passed to \link{ggpar}().}
}
\description{
Plot paired data.
}
\examples{

# Example 1
# ::::::::::::::::::::::::::::::::::::::::::
before <- c(200.1, 190.9, 192.7, 213, 241.4, 196.9, 172.2, 185.5, 205.2, 193.7)
after <- c(392.9, 393.2, 345.1, 393, 434, 427.9, 422, 383.9, 392.3, 352.2)

d <- data.frame(before = before, after = after)
ggpaired(d,
  cond1 = "before", cond2 = "after",
  fill = "condition", palette = "jco"
)

# Example 2
# ::::::::::::::::::::::::::::::::::::::::::
ggpaired(ToothGrowth,
  x = "supp", y = "len",
  color = "supp", line.color = "gray", line.size = 0.4,
  palette = "npg"
)

}
