plot.clonal.models: Plot evolution models (polygon plots and trees) for multi...
In hadaxu/clonevol-mirror: What the package does (one line)

Description Usage Arguments

Plot evolution models inferred by infer.clonal.models function Two types of plots are supported: polygon plot and tree plot

## S3 method for class 'clonal.models'
plot(models, out.dir, matched = NULL,
  variants = NULL, box.plot = FALSE, cluster.col.name = "cluster",
  scale.monoclonal.cell.frac = TRUE, width = NULL, height = NULL,
  text.size = 1, tree.node.shape = "circle", tree.node.size = 50,
  tree.node.text.size = 1, out.format = "png", resolution = 300,
  overwrite.output = FALSE, max.num.models.to.plot = 10,
  cell.frac.ci = FALSE, show.score = T, out.prefix = "model")

`models:`	list of model output from infer.clonal.models function
`out.dir:`	output directory for the plots
`matched:`	data frame of compatible models for multiple samples
`scale.monoclonal.cell.frac:`	c(TRUE, FALSE); if TRUE, scale cellular fraction in the plots (ie. cell fraction will be scaled by 1/purity = 1/max(VAF*2))
`width:`	width of the plots (in), if NULL, automatically choose width
`height:`	height of the plots (in), if NULL, automatically choose height
`out.format:`	format of the plot files ('png', 'pdf', 'pdf.multi.files')
`resolution:`	resolution of the PNG plot file
`overwrite.output:`	if TRUE, overwrite output directory, default=FALSE
`max.num.models.to.plot:`	max number of models to plot; default = 100 if NULL, unlimited