plotCNprofile.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotting.R
\name{plotCNprofile}
\alias{plotCNprofile}
\title{Plot a single cell copy number profile}
\usage{
plotCNprofile(
  CNbins,
  cellid = NULL,
  chrfilt = NULL,
  pointsize = 1,
  alphaval = 0.6,
  maxCN = 10,
  cellidx = 1,
  statecol = "state",
  returnlist = FALSE,
  raster = FALSE,
  genome = "hg19",
  y_axis_trans = "identity",
  xaxis_order = "genome_position",
  legend.position = "bottom",
  annotateregions = NULL,
  annotateregions_linetype = 2,
  SV = NULL,
  SVcol = TRUE,
  svalpha = 0.5,
  svwidth = 1,
  adj = 0.03,
  genes = NULL,
  tickwidth = 50,
  chrstart = NULL,
  chrend = NULL,
  shape = 16,
  positionticks = FALSE,
  ideogram = FALSE,
  overwrite_color = NULL,
  ...
)
}
\arguments{
\item{CNbins}{Single cell copy number dataframe with the following columns: \code{cell_id}, \code{chr}, \code{start}, \code{end}, \code{state}, \code{copy}}

\item{cellid}{Which cell to plot, if no cell is specific will plot the first cell in the dataframe}

\item{chrfilt}{Vector of chromosomes to plot, if NULL (default) will plot all chromosomes}

\item{pointsize}{The point size in the plot}

\item{alphaval}{Alpha value of points}

\item{maxCN}{The maximum on the y axis, if any points are above this value they will be winsorized rather than removed}

\item{cellidx}{idx of cell to plot if cellid = NULL}

\item{statecol}{The colour mapping, default is to map colours to the \code{state} column}

\item{returnlist}{Return a list rather than the ggplot object}

\item{raster}{use ggrastr or not, default = FALSE}

\item{genome}{genome to use, default = "hg19" (only used for ideogram)}

\item{y_axis_trans}{What transformation to use on the y-axis, default is identity, the other option is "squashy" which uses a tanh transformation}

\item{xaxis_order}{Default is "genome_position"}

\item{legend.position}{Where to place the legend, default is "bottom"}

\item{annotateregions}{Dataframe with chr start and end positions to annotate, will draw a dashed vertical line at this position}

\item{annotateregions_linetype}{linetype for region annotation, default = 2 (dashed)}

\item{SV}{Default is NULL. If a dataframe with structural variant position is passed it will add rearrangement links between bins.}

\item{SVcol}{Default is TRUE. Colour SVs or not}

\item{svalpha}{the alpha scaling of the SV lines, default = 0.5}

\item{svwidth}{Width of SV width curves, default = 1.0}

\item{adj}{adjustment for gene labels}

\item{genes}{vector of genes to annotate, will add a dashed vertical line and label}

\item{tickwidth}{Spacing of ticks (in Mb) when only 1 chromosome is plotted}

\item{chrstart}{Start of region (in Mb) when plotting a single chromosome}

\item{chrend}{End of region (in Mb) when plotting a single chromosome}

\item{shape}{shape for plotting, default = 16}

\item{positionticks}{set to TRUE to use position ticks rather than chromosome ticks}

\item{ideogram}{plot ideogram at the top, default = TRUE}
}
\value{
ggplot2 plot
}
\description{
Plot a single cell copy number profile
}
\examples{

plotCNprofile(CNbins)
}