plotCNprofile: Plot a single cell copy number profile
In shahcompbio/signals: Single Cell Genomes with Allele Specificity

plotCNprofile

R Documentation

Plot a single cell copy number profile

Description

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

`CNbins`	Single cell copy number dataframe with the following columns: `cell_id`, `chr`, `start`, `end`, `state`, `copy`
`cellid`	Which cell to plot, if no cell is specific will plot the first cell in the dataframe
`chrfilt`	Vector of chromosomes to plot, if NULL (default) will plot all chromosomes
`pointsize`	The point size in the plot
`alphaval`	Alpha value of points
`maxCN`	The maximum on the y axis, if any points are above this value they will be winsorized rather than removed
`cellidx`	idx of cell to plot if cellid = NULL
`statecol`	The colour mapping, default is to map colours to the `state` column
`returnlist`	Return a list rather than the ggplot object
`raster`	use ggrastr or not, default = FALSE
`genome`	genome to use, default = "hg19" (only used for ideogram)
`y_axis_trans`	What transformation to use on the y-axis, default is identity, the other option is "squashy" which uses a tanh transformation
`xaxis_order`	Default is "genome_position"
`legend.position`	Where to place the legend, default is "bottom"
`annotateregions`	Dataframe with chr start and end positions to annotate, will draw a dashed vertical line at this position
`annotateregions_linetype`	linetype for region annotation, default = 2 (dashed)
`SV`	Default is NULL. If a dataframe with structural variant position is passed it will add rearrangement links between bins.
`SVcol`	Default is TRUE. Colour SVs or not
`svalpha`	the alpha scaling of the SV lines, default = 0.5
`svwidth`	Width of SV width curves, default = 1.0
`adj`	adjustment for gene labels
`genes`	vector of genes to annotate, will add a dashed vertical line and label
`tickwidth`	Spacing of ticks (in Mb) when only 1 chromosome is plotted
`chrstart`	Start of region (in Mb) when plotting a single chromosome
`chrend`	End of region (in Mb) when plotting a single chromosome
`shape`	shape for plotting, default = 16
`positionticks`	set to TRUE to use position ticks rather than chromosome ticks
`ideogram`	plot ideogram at the top, default = TRUE