% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ggbarplot.R
\name{ggbarplot}
\alias{ggbarplot}
\title{Bar plot}
\usage{
ggbarplot(
  data,
  x,
  y,
  combine = FALSE,
  merge = FALSE,
  color = "black",
  fill = "white",
  palette = NULL,
  size = NULL,
  width = NULL,
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  facet.by = NULL,
  panel.labs = NULL,
  short.panel.labs = TRUE,
  select = NULL,
  remove = NULL,
  order = NULL,
  add = "none",
  add.params = list(),
  error.plot = "errorbar",
  label = FALSE,
  lab.col = "black",
  lab.size = 4,
  lab.pos = c("out", "in"),
  lab.vjust = NULL,
  lab.hjust = NULL,
  lab.nb.digits = NULL,
  sort.val = c("none", "desc", "asc"),
  sort.by.groups = TRUE,
  top = Inf,
  position = position_stack(),
  numeric.x.axis = FALSE,
  ggtheme = theme_pubr(),
  ...
)
}
\arguments{
\item{data}{a data frame}

\item{x, y}{x and y variables for drawing.}

\item{combine}{logical value. Default is FALSE. Used only when y is a vector
containing multiple variables to plot. If TRUE, create a multi-panel plot by
combining the plot of y variables.}

\item{merge}{logical or character value. Default is FALSE. Used only when y is
a vector containing multiple variables to plot. If TRUE, merge multiple y
variables in the same plotting area. Allowed values include also "asis"
(TRUE) and "flip". If merge = "flip", then y variables are used as x tick
labels and the x variable is used as grouping variable.}

\item{color, fill}{outline and fill colors.}

\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{size}{Numeric value (e.g.: size = 1). change the size of points and
outlines.}

\item{width}{numeric value between 0 and 1 specifying the width of the plot elements.}

\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{select}{character vector specifying which items to display.}

\item{remove}{character vector specifying which items to remove from the plot.}

\item{order}{character vector specifying the order of items.}

\item{add}{character vector for adding another plot element (e.g.: dot plot or
error bars). Allowed values are one or the combination of: "none",
"dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd",
"mean_ci", "mean_range", "median", "median_iqr", "median_hilow",
"median_q1q3", "median_mad", "median_range"; see ?desc_statby for more
details.}

\item{add.params}{parameters (color, shape, size, fill, linetype) for the
argument 'add'; e.g.: add.params = list(color = "red").}

\item{error.plot}{plot type used to visualize error. Allowed values are one of
c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar",
"lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange",
"lower_linerange"). Default value is "pointrange" or "errorbar". Used only
when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd,
se, ....}

\item{label}{specify whether to add labels on the bar plot. Allowed values
are: \itemize{ \item \strong{logical value}: If TRUE, y values are added as
labels on the bar plot \item \strong{character vector}: Used as text
labels; must be the same length as y. }}

\item{lab.col, lab.size}{text color and size for labels.}

\item{lab.pos}{character specifying the position for labels. Allowed values
are "out" (for outside) or "in" (for inside). Ignored when lab.vjust !=
NULL.}

\item{lab.vjust}{numeric, vertical justification of labels. Provide negative
value (e.g.: -0.4) to put labels outside the bars or positive value to put
labels inside (e.g.: 2).}

\item{lab.hjust}{numeric, horizontal justification of labels.}

\item{lab.nb.digits}{integer indicating the number of decimal places (round) to be used.}

\item{sort.val}{a string specifying whether the value should be sorted.
Allowed values are "none" (no sorting), "asc" (for ascending) or "desc" (for descending).}

\item{sort.by.groups}{logical value. If TRUE the data are sorted by groups.
Used only when sort.val != "none".}

\item{top}{a numeric value specifying the number of top elements to be shown.}

\item{position}{position adjustment, either as a string, or the result of a
call to a position adjustment function (e.g. \code{position_dodge(0.8)}).
Used to control the spacing between grouped elements.}

\item{numeric.x.axis}{logical. If TRUE, x axis will be treated as numeric.
Default is FALSE. Useful, for example, to plot bars at their numeric x
positions (e.g. a time axis) instead of at equally-spaced discrete
categories. Ignored when \code{order} is set or \code{sort.val != "none"},
which require a discrete x axis.}

\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{...}{other arguments to be passed to be passed to ggpar().}
}
\description{
Create a bar plot.
}
\details{
The plot can be easily customized using the function ggpar(). Read
  ?ggpar for changing: \itemize{ \item main title and axis labels: main,
  xlab, ylab \item axis limits: xlim, ylim (e.g.: ylim = c(0, 30)) \item axis
  scales: xscale, yscale (e.g.: yscale = "log2") \item color palettes:
  palette = "Dark2" or palette = c("gray", "blue", "red") \item legend title,
  labels and position: legend = "right" \item plot orientation : orientation
  = c("vertical", "horizontal", "reverse") }
}
\section{Faceting a summarized bar plot}{

When the bars show a computed summary (e.g. \code{add = "mean_se"}), facet the
plot with the \code{facet.by} argument - \strong{not} by appending
\code{+ facet_wrap()} / \code{+ facet_grid()}. The summaries are pre-computed,
grouping by \code{x}, \code{color}/\code{fill} and \code{facet.by}; a facet added
afterwards is not part of that grouping, so the bars (and, for stacked bars, the
error bars) are pooled over the whole data set and repeated identically in every
panel. Use \code{ggbarplot(..., facet.by = "group")} for correct per-panel
summaries.
}

\examples{
# Data
df <- data.frame(
  dose = c("D0.5", "D1", "D2"),
  len = c(4.2, 10, 29.5)
)
print(df)

# Basic plot with label outsite
# +++++++++++++++++++++++++++
ggbarplot(df,
  x = "dose", y = "len",
  label = TRUE, label.pos = "out"
)

# Change width
ggbarplot(df, x = "dose", y = "len", width = 0.5)

# Change the plot orientation: horizontal
ggbarplot(df, "dose", "len", orientation = "horiz")

# Change the default order of items
ggbarplot(df, "dose", "len",
  order = c("D2", "D1", "D0.5")
)


# Change colors
# +++++++++++++++++++++++++++

# Change fill and outline color
# add labels inside bars
ggbarplot(df, "dose", "len",
  fill = "steelblue", color = "steelblue",
  label = TRUE, lab.pos = "in", lab.col = "white"
)

# Change colors by groups: dose
# Use custom color palette
ggbarplot(df, "dose", "len",
  color = "dose",
  palette = c("#00AFBB", "#E7B800", "#FC4E07")
)

# Change fill and outline colors by groups
ggbarplot(df, "dose", "len",
  fill = "dose", color = "dose",
  palette = c("#00AFBB", "#E7B800", "#FC4E07")
)


# Plot with multiple groups
# +++++++++++++++++++++

# Create some data
df2 <- data.frame(
  supp = rep(c("VC", "OJ"), each = 3),
  dose = rep(c("D0.5", "D1", "D2"), 2),
  len = c(6.8, 15, 33, 4.2, 10, 29.5)
)
print(df2)

# Plot "len" by "dose" and change color by a second group: "supp"
# Add labels inside bars
ggbarplot(df2, "dose", "len",
  fill = "supp", color = "supp", palette = "Paired",
  label = TRUE, lab.col = "white", lab.pos = "in"
)

# Change position: Interleaved (dodged) bar plot
ggbarplot(df2, "dose", "len",
  fill = "supp", color = "supp", palette = "Paired",
  label = TRUE,
  position = position_dodge(0.9)
)

# Add points and errors
# ++++++++++++++++++++++++++

# Data: ToothGrowth data set we'll be used.
df3 <- ToothGrowth
head(df3, 10)

# It can be seen that for each group we have
# different values
ggbarplot(df3, x = "dose", y = "len")

# Visualize the mean of each group
ggbarplot(df3,
  x = "dose", y = "len",
  add = "mean"
)

# Add error bars: mean_se
# (other values include: mean_sd, mean_ci, median_iqr, ....)
# Add labels
ggbarplot(df3,
  x = "dose", y = "len",
  add = "mean_se", label = TRUE, lab.vjust = -1.6
)

# Use only "upper_errorbar"
ggbarplot(df3,
  x = "dose", y = "len",
  add = "mean_se", error.plot = "upper_errorbar"
)

# Change error.plot to "pointrange"
ggbarplot(df3,
  x = "dose", y = "len",
  add = "mean_se", error.plot = "pointrange"
)

# Add jitter points and errors (mean_se)
ggbarplot(df3,
  x = "dose", y = "len",
  add = c("mean_se", "jitter")
)

# Add dot and errors (mean_se)
ggbarplot(df3,
  x = "dose", y = "len",
  add = c("mean_se", "dotplot")
)

# Multiple groups with error bars and jitter point
ggbarplot(df3,
  x = "dose", y = "len", color = "supp",
  add = "mean_se", palette = c("#00AFBB", "#E7B800"),
  position = position_dodge()
)
#

}
\seealso{
\code{\link{ggpar}}, \code{\link{ggline}}
}
