plotCNprofileBAF: Plot a single cell allele specific copy number profile

In shahcompbio/signals: Single Cell Genomes with Allele Specificity

Plot a single cell allele specific copy number profile

Description

Plot a single cell allele specific copy number profile

Usage

plotCNprofileBAF(
  cn,
  cellid = NULL,
  chrfilt = NULL,
  pointsize = 1,
  alphaval = 0.6,
  maxCN = 10,
  cellidx = 1,
  BAFcol = "state_phase",
  statecol = "state",
  returnlist = FALSE,
  raster = FALSE,
  y_axis_trans = "identity",
  xaxis_order = "genome_position",
  legend.position = "bottom",
  genes = NULL,
  annotateregions = NULL,
  annotateregions_linetype = 2,
  homolog = FALSE,
  SV = NULL,
  adj = 0.03,
  svalpha = 0.5,
  svwidth = 1,
  plotdata = TRUE,
  offset = NULL,
  my_title = NULL,
  tickwidth = 50,
  chrstart = NULL,
  chrend = NULL,
  shape = 16,
  ideogram = FALSE,
  positionticks = FALSE,
  genome = "hg19",
  ...
)

Arguments

cn	Single cell allele specific copy number dataframe with the following columns: 'cell_id', 'chr', 'start', 'end', 'state', 'copy' or a hscn object.
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
BAFcol	state to use to colour BAF track, default = 'state_phase'
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
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"
genes	vector of genes to annotate, will add a dashed vertical line and label
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)
homolog	Rather than plot the BAF and CN seperately this will plot the 2 homologs on the same track
SV	Default is NULL. If a dataframe with structural variant position is passed it will add a track on the top showin rearrangement links
svalpha	the alpha scaling of the SV lines, default = 0.5
svwidth	width of rearrangement connections
plotdata	Binary value whether to plot raw data or inferred states in homolog plot
my_title	string to use for title, if NULL cell_id is shown
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
ideogram	plot ideogram at the top, default = TRUE
positionticks	set to TRUE to use position ticks rather than chromosome ticks
genome	genome to use, default = "hg19" (only used for ideogram)
offest	to use when plotting inferred states in homolog plot

Value

ggplot2 plot

Examples

## Not run: 
data("haplotypes")
data("CNbins")
haplotypes <- format_haplotypes_dlp(haplotypes, CNbins)
hscn <- callHaplotypeSpecificCN(CNbins, haplotypes, likelihood = "binomial")
plotCNprofileBAF(hscn, genes = "MYC")
plotCNprofileBAF(hscn, homolog = TRUE, chrfilt = c("1", "8"))

## End(Not run)

shahcompbio/signals documentation built on Jan. 11, 2025, 2:20 a.m.