tronco.plot {TRONCO} | R Documentation |
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, ... )
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 |
Information about the reconstructed model
data(test_model) tronco.plot(test_model)