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