% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/upsetplot.R
\name{UpsetPlotAtomic}
\alias{UpsetPlotAtomic}
\title{Atomic Upset plot}
\usage{
UpsetPlotAtomic(
  data,
  in_form = "auto",
  group_by = NULL,
  group_by_sep = "_",
  id_by = NULL,
  label = TRUE,
  label_fg = "black",
  label_size = NULL,
  label_bg = "white",
  label_bg_r = 0.1,
  palette = "material-indigo",
  palcolor = NULL,
  alpha = 1,
  specific = TRUE,
  combmatrix_gap = 6,
  theme = "theme_this",
  theme_args = list(),
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  aspect.ratio = 0.6,
  legend.position = "right",
  legend.direction = "vertical",
  levels = NULL,
  ...
)
}
\arguments{
\item{data}{A data frame.}

\item{in_form}{A character string indicating the datatype of the input data.
Possible values are "long", "wide", "list", "upset" or "auto".
"long" indicates the data is in long format.
"wide" indicates the data is in wide format.
"list" indicates the data is a list.
"upset" indicates the data is a UpsetPlotData object.
"auto" indicates the function will detect the datatype of the input data.

A long format data would look like:
\preformatted{
group_by id_by
A        a1
A        a2
B        a1
B        a3
...
}

A wide format data would look like:
\preformatted{
A    B
TRUE TRUE
TRUE FALSE
FALSE TRUE
...
}

A list format data would look like:
\preformatted{
list(A = c("a1", "a2"), B = c("a1", "a3"))
}

An UpsetPlotData object is generated by prepare_update_data() would look like:
\preformatted{
group_by
--------
list("A")  # a2
list("B")  # a3
list(c("A", "B"))  # a1
...
}}

\item{group_by}{Columns to group the data for plotting
For those plotting functions that do not support multiple groups,
They will be concatenated into one column, using \code{group_by_sep} as the separator}

\item{group_by_sep}{The separator for multiple group_by columns. See \code{group_by}}

\item{id_by}{A character string specifying the column name of the data frame to identify the instances.
Required when \code{group_by} is a single column and data is a data frame.}

\item{label}{A logical value to show the labels on the bars.}

\item{label_fg}{A character string specifying the color of the label text.}

\item{label_size}{A numeric value specifying the size of the label text.}

\item{label_bg}{A character string specifying the background color of the label.}

\item{label_bg_r}{A numeric value specifying the radius of the background of the label.}

\item{palette}{A character string specifying the palette to use.
A named list or vector can be used to specify the palettes for different \code{split_by} values.}

\item{palcolor}{A character string specifying the color to use in the palette.
A named list can be used to specify the colors for different \code{split_by} values.
If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).}

\item{alpha}{A numeric value specifying the transparency of the plot.}

\item{specific}{A logical value to show the specific intersections only.
ggVennDiagram, by default, only return the specific subsets of a region. However,
sometimes, we want to show all the overlapping items for two or more sets.
See \url{https://github.com/gaospecial/ggVennDiagram/issues/64} for more details.}

\item{combmatrix_gap}{A numeric value specifying the gap between the rows of the combination matrix.
The default value is 6, which is suitable for a base_size of 12.
The actual gap will be scaled by the text size scale, which is calculated as base_size / 12.}

\item{theme}{A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use.
Default is "theme_this".}

\item{theme_args}{A list of arguments to pass to the theme function.}

\item{title}{A character string specifying the title of the plot.
A function can be used to generate the title based on the default title.
This is useful when split_by is used and the title needs to be dynamic.}

\item{subtitle}{A character string specifying the subtitle of the plot.}

\item{xlab}{A character string specifying the x-axis label.}

\item{ylab}{A character string specifying the y-axis label.}

\item{aspect.ratio}{A numeric value specifying the aspect ratio of the plot.}

\item{legend.position}{A character string specifying the position of the legend.
if \code{waiver()}, for single groups, the legend will be "none", otherwise "right".}

\item{legend.direction}{A character string specifying the direction of the legend.}

\item{...}{Additional arguments passed to \link[ggupset:scale_x_upset]{ggupset::scale_x_upset}.}
}
\value{
A ggplot object with Upset plot
}
\description{
Atomic Upset plot
}
\keyword{internal}
