tronco.plot {TRONCO} | R Documentation

## tronco.plot

### 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)

[Package TRONCO version 2.26.0 Index]