plotModel: Plot a model

In saezlab/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Plot a model

Description

This function can be used to plot a prior model network before any pre-processing step. However, additional information can be provided such as a CNOlist (see makeCNOlist and readMIDAS) or information related to the pre-processing steps (compression, NONC nodes, expansion gates). It can also be used to plot optimised model given the optimisation bitstring.

Usage

plotModel(model, CNOlist=NULL, bString=NULL, indexIntegr=NULL, signals=NULL, 
stimuli=NULL, inhibitors=NULL, NCNO=NULL, compressed=NULL, output="STDOUT",
filename=NULL, graphvizParams=list(), show=TRUE, remove_dot=TRUE, removeEmptyAnds=TRUE)

Arguments

model	a model as returned by readSIF. Alternatively, the filename can also be provided.
CNOlist	output of makeCNOlist
bString	a sequence made of numbers between 0 and 1 of same length as the one returned by the Genetic Algorithm (GA). This is a generalisation of the bitString returned by the GA function: several bit strings can be averaged and used.
indexIntegr	additional indices to highlight some edge (optional).
signals	a list of nodes belonging to the signals class
stimuli	a list of nodes belonging to the stimuli class
inhibitors	a list of nodes belonging to the inhibitors class
NCNO	a list of NCNO nodes.
compressed	a list of compressed nodes
filename	the filename (without extension) used to write the dot file
output	the type of output (PNG, PDF, SVG accepted)
graphvizParams	a list of optional arguments dedicated to Rgraphviz to tune the layout: arrowsize default is 2 sizea string for the size of the dot output; default is "15,15" fontsize default is 22 edgecolor default is "black" nodeLabels overwrit node label with a list of proper length. nodeWidth default is 2 nodeHeight default is 1 viewEmptyEdges default is TRUE mode can be 'classic' or 'sbgn' (default). The difference appears in the and gate. andWidth = 0.2 in 'classic' mode and 0.5 in 'sbgn' mode andHeight = 0.2 in 'classic' mode and 0.5 in 'sbgn' mode
show	show the plot (default is True)
remove_dot	remove the dot file that has been created. Default is False
removeEmptyAnds	removes AND gates from plotted graph if the corresponding bit is 0 to give a compact view. Default is TRUE.

Details

This function plots the model and also saves it in a dot file that can be processed later on. However, you can also save the plot in PNG or PDF or SVG format (one at a time).

The CNOlist argument contains the signals/stimuli/inhibitors so if you provide a CNOlist there is no need to use these arguments. If you decide to use them they will overwrite the contents of the CNOlist argument.

optimRes is the output of gaBinary. One of its field is called bString and contains a list of 0 and 1 (the optimisation is perfomed with a binary procedure). This list of 0 and 1 is then used to plot or not the edges of the model. However, you can provide a bitString made of floats (e.g., average of several bitStrings). In such case, edges will appear in gray light or dark according to the bistring value (between 0 and 1).

Value

a graph representation of the model

graph$g	A graph representation of the model
graph$attrs	graph attributes
graph$nodeAttrs	nodes attributes
graph$edgeAttrs	edges attributes
graph$clusters	clusters of nodes

Note

This function depends on the Rgraphviz package.

Author(s)

T. Cokelaer

See Also

readMIDAS, readSIF, makeCNOlist, writeNetwork, writeDot, gaBinaryT1

Examples

    data(CNOlistToy,package="CellNOptR")
    data(ToyModel,package="CellNOptR")
    res<-plotModel(ToyModel, CNOlist=CNOlistToy, compressed=c("TRAF6", "p38"), 
        graphvizParams=list(mode="classic", fontsize=30))
    

saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.