% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/do_CopyNumberVariantPlot.R
\name{do_CopyNumberVariantPlot}
\alias{do_CopyNumberVariantPlot}
\title{Display CNV scores from inferCNV as Feature Plots.}
\usage{
do_CopyNumberVariantPlot(
  sample,
  infercnv_object,
  chromosome_locations,
  group.by = NULL,
  using_metacells = FALSE,
  metacell_mapping = NULL,
  include_chr_arms = FALSE,
  legend.type = "colorbar",
  legend.position = "bottom",
  legend.length = 20,
  legend.width = 1,
  legend.framewidth = 0.5,
  legend.tickwidth = 0.5,
  legend.framecolor = "grey50",
  legend.tickcolor = "white",
  font.size = 14,
  pt.size = 1,
  font.type = "sans",
  axis.text.x.angle = 45,
  enforce_symmetry = TRUE,
  legend.title = NULL,
  na.value = "grey75",
  viridis.palette = "G",
  viridis.direction = 1,
  verbose = FALSE,
  min.cutoff = NA,
  max.cutoff = NA,
  number.breaks = 5,
  diverging.palette = "RdBu",
  diverging.direction = -1,
  sequential.palette = "YlGnBu",
  sequential.direction = -1,
  use_viridis = TRUE,
  return_object = FALSE,
  grid.color = "white",
  border.color = "black",
  flip = FALSE,
  plot.title.face = "bold",
  plot.subtitle.face = "plain",
  plot.caption.face = "italic",
  axis.title.face = "bold",
  axis.text.face = "plain",
  legend.title.face = "bold",
  legend.text.face = "plain"
)
}
\arguments{
\item{sample}{\strong{\code{\link[SeuratObject]{Seurat}}} | A Seurat object, generated by \link[Seurat]{CreateSeuratObject}.}

\item{infercnv_object}{\strong{\code{\link[infercnv]{infercnv}}} | Output inferCNV object run on the same Seurat object.}

\item{chromosome_locations}{\strong{\code{\link[tibble]{tibble}}} | Tibble containing the chromosome regions to use. Can be obtained using \strong{\code{utils::data("human_chr_locations", package = "SCpubr")}}.}

\item{group.by}{\strong{\code{\link[base]{character}}} | Metadata variable to group the output by. Has to be a character of factor column.}

\item{using_metacells}{\strong{\code{\link[base]{logical}}} | Whether inferCNV was run using metacells or not.}

\item{metacell_mapping}{\strong{\code{\link[SCpubr]{named_vector}}} | Vector or cell - metacell mapping.}

\item{include_chr_arms}{\strong{\code{\link[base]{logical}}} | Whether the output heatmap should also include chromosome arms or just whole chromosomes.}

\item{legend.type}{\strong{\code{\link[base]{character}}} | Type of legend to display. One of:
\itemize{
\item \emph{\code{normal}}: Default legend displayed by \pkg{ggplot2}.
\item \emph{\code{colorbar}}: Redefined colorbar legend, using \link[ggplot2]{guide_colorbar}.
}}

\item{legend.position}{\strong{\code{\link[base]{character}}} | Position of the legend in the plot. One of:
\itemize{
\item \emph{\code{top}}: Top of the figure.
\item \emph{\code{bottom}}: Bottom of the figure.
\item \emph{\code{left}}: Left of the figure.
\item \emph{\code{right}}: Right of the figure.
\item \emph{\code{none}}: No legend is displayed.
}}

\item{legend.length, legend.width}{\strong{\code{\link[base]{numeric}}} | Length and width of the legend. Will adjust automatically depending on legend side.}

\item{legend.framewidth, legend.tickwidth}{\strong{\code{\link[base]{numeric}}} | Width of the lines of the box in the legend.}

\item{legend.framecolor}{\strong{\code{\link[base]{character}}} | Color of the lines of the box in the legend.}

\item{legend.tickcolor}{\strong{\code{\link[base]{character}}} | Color of the ticks of the box in the legend.}

\item{font.size}{\strong{\code{\link[base]{numeric}}} | Overall font size of the plot. All plot elements will have a size relationship with this font size.}

\item{pt.size}{\strong{\code{\link[base]{numeric}}} | Size of the dots.}

\item{font.type}{\strong{\code{\link[base]{character}}} | Base font family for the plot. One of:
\itemize{
\item \emph{\code{mono}}: Mono spaced font.
\item \emph{\code{serif}}: Serif font family.
\item \emph{\code{sans}}: Default font family.
}}

\item{axis.text.x.angle}{\strong{\code{\link[base]{numeric}}} | Degree to rotate the X labels. One of: 0, 45, 90.}

\item{enforce_symmetry}{\strong{\code{\link[base]{logical}}} | Return a symmetrical plot axes-wise or continuous color scale-wise, when applicable.}

\item{legend.title}{\strong{\code{\link[base]{character}}} | Title for the legend.}

\item{na.value}{\strong{\code{\link[base]{character}}} | Color value for NA.}

\item{viridis.palette}{\strong{\code{\link[base]{character}}} | A capital letter from A to H or the scale name as in \link[viridis]{scale_fill_viridis}.}

\item{viridis.direction}{\strong{\code{\link[base]{numeric}}} | Either 1 or -1. Controls how the gradient of viridis scale is formed.}

\item{verbose}{\strong{\code{\link[base]{logical}}} | Whether to show extra comments, warnings,etc.}

\item{min.cutoff, max.cutoff}{\strong{\code{\link[base]{numeric}}} | Set the min/max ends of the color scale. Any cell/group with a value lower than min.cutoff will turn into min.cutoff and any cell with a value higher than max.cutoff will turn into max.cutoff. In FeaturePlots, provide as many values as features. Use NAs to skip a feature.}

\item{number.breaks}{\strong{\code{\link[base]{numeric}}} | Controls the number of breaks in continuous color scales of ggplot2-based plots.}

\item{diverging.palette}{\strong{\code{\link[base]{character}}} | Type of symmetrical color palette to use. Out of the diverging palettes defined in \strong{\code{\link[RColorBrewer]{brewer.pal}}}.}

\item{diverging.direction}{\strong{\code{\link[base]{numeric}}} | Either 1 or -1. Direction of the divering palette. This basically flips the two ends.}

\item{sequential.palette}{\strong{\code{\link[base]{character}}} | Type of sequential color palette to use. Out of the sequential palettes defined in \strong{\code{\link[RColorBrewer]{brewer.pal}}}.}

\item{sequential.direction}{\strong{\code{\link[base]{numeric}}} | Direction of the sequential color scale. Either 1 or -1.}

\item{use_viridis}{\strong{\code{\link[base]{logical}}} | Whether to use viridis color scales.}

\item{return_object}{\strong{\code{\link[base]{logical}}} | Returns the Seurat object with the modifications performed in the function. Nomally, this contains a new assay with the data that can then be used for any other visualization desired.}

\item{grid.color}{\strong{\code{\link[base]{character}}} | Color of the grid in the plot. In heatmaps, color of the border of the cells.}

\item{border.color}{\strong{\code{\link[base]{character}}} | Color for the border of the heatmap body.}

\item{flip}{\strong{\code{\link[base]{logical}}} | Whether to invert the axis of the displayed plot.}

\item{plot.title.face, plot.subtitle.face, plot.caption.face, axis.title.face, axis.text.face, legend.title.face, legend.text.face}{\strong{\code{\link[base]{character}}} | Controls the style of the font for the corresponding theme element.  One of:
\itemize{
\item \emph{\code{plain}}: For normal text.
\item \emph{\code{italic}}: For text in itallic.
\item \emph{\code{bold}}: For text in bold.
\item \emph{\code{bold.italic}}: For text both in itallic and bold.
}}
}
\value{
A list containing Feature Plots for different chromosome regions and corresponding dot plots by groups..
}
\description{
Display CNV scores from inferCNV as Feature Plots.
}
\examples{
\donttest{
  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_CopyNumberVariantPlot", passive = TRUE)

  if (isTRUE(value)){
    # Consult the full documentation in https://enblacar.github.io/SCpubr-book/

    # This function expects that you have run inferCNV on your
    # own and you have access to the output object.

    # Define your Seurat object.
    sample <- readRDS(system.file("extdata/seurat_dataset_example.rds",
                                  package = "SCpubr"))

    # Define your inferCNV object.
    infercnv_object <- readRDS(system.file("extdata/infercnv_object_example.rds",
                                           package = "SCpubr"))

    # Get human chromosome locations.
    chromosome_locations = SCpubr::human_chr_locations

    # Compute for a all chromosomes.
    p <- SCpubr::do_CopyNumberVariantPlot(sample = sample,
                                          infercnv_object = infercnv_object,
                                          using_metacells = FALSE,
                                          chromosome_locations = chromosome_locations)

  } else if (base::isFALSE(value)){
    message("This function can not be used without its suggested packages.")
    message("Check out which ones are needed using `SCpubr::state_dependencies()`.")
  }
}
}
