R Graphical Manual

Browse All

Last data update: 2014.03.03

R: tronco.plot

tronco.plot

R Documentation

tronco.plot

Description

Plots a progression model from a recostructed dataset

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, ...)

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 igraph object generated
`...`	Additional arguments for RGraphviz plot function

Value

Information about the reconstructed model

Examples

data(test_model)
tronco.plot(test_model)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(TRONCO)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TRONCO/tronco.plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: tronco.plot
> ### Title: tronco.plot
> ### Aliases: tronco.plot
> 
> ### ** Examples
> 
> data(test_model)
> tronco.plot(test_model)
*** Expanding hypotheses syntax as graph nodes:
*** Rendering graphics
Nodes with no incoming/outgoing edges will not be displayed.
RGraphviz object prepared.
Plotting graph and adding legends.

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>