tronco.plot: tronco.plot

In TRONCO: TRONCO, an R package for TRanslational ONCOlogy

Description

Plots a progression model from a recostructed dataset. For details and examples regarding the visualization of an inferred model, we refer to the Vignette Section 7.

Usage

tronco.plot(
  x,
  models = names(x$model),
  fontsize = NA,
  height = 2,
  width = 3,
  height.logic = 1,
  pf = FALSE,
  disconnected = FALSE,
  scale.nodes = NA,
  title = as.description(x),
  confidence = NA,
  p.min = 0.05,
  legend = TRUE,
  legend.cex = 1,
  edge.cex = 1,
  label.edge.size = NA,
  expand = TRUE,
  genes = NULL,
  relations.filter = NA,
  edge.color = "black",
  pathways.color = "Set1",
  file = NA,
  legend.pos = "bottom",
  pathways = NULL,
  lwd = 3,
  samples.annotation = NA,
  export.igraph = FALSE,
  create.new.dev = TRUE,
  ...
)

Arguments

x	A reconstructed model (the output of the inference by a tronco function)
models	A vector containing the names of the algorithms used (caprese, capri_bic, etc)
fontsize	For node names. Default NA for automatic rescaling
height	Proportion node height - node width. Default height 2
width	Proportion node height - node width. Default width 2
height.logic	Height of logical nodes. Defaul 1
pf	Should I print Prima Facie? Default False
disconnected	Should I print disconnected nodes? Default False
scale.nodes	Node scaling coefficient (based on node frequency). Default NA (autoscale)
title	Title of the plot. Default as.description(x)
confidence	Should I add confidence informations? No if NA
p.min	p-value cutoff. Default automatic
legend	Should I visualise the legend?
legend.cex	CEX value for legend. Default 1.0
edge.cex	CEX value for edge labels. Default 1.0
label.edge.size	Size of edge labels. Default NA for automatic rescaling
expand	Should I expand hypotheses? Default TRUE
genes	Visualise only genes in this list. Default NULL, visualise all.
relations.filter	Filter relations to dispaly according to this functions. Default NA
edge.color	Edge color. Default 'black'
pathways.color	RColorBrewer colorser for patways. Default 'Set1'.
file	String containing filename for PDF output. If NA no PDF output will be provided
legend.pos	Legend position. Default 'bottom',
pathways	A vector containing pathways information as described in as.patterns()
lwd	Edge base lwd. Default 3
samples.annotation	= List of samples to search for events in model
export.igraph	If TRUE export the generated igraph object
create.new.dev	If TRUE create a new graphical device when calling trono.plot. Set this to FALSE, e.g., if you do not wish to create a new device when executing the command with export.igraph = TRUE
...	Additional arguments for RGraphviz plot function

Value

Information about the reconstructed model

Examples

data(test_model)
tronco.plot(test_model)

TRONCO documentation built on Nov. 8, 2020, 5:51 p.m.