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.
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)
#> *** 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.
#> Warning: font metrics unknown for character 0x0a in encoding latin1
#> Warning: font metrics unknown for character 0x0a in encoding latin1
#>