Plot a model

Share:

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

1
2
3
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)

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 if False)

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

1
2
3
4
5
    data(CNOlistToy,package="CellNOptR")
    data(ToyModel,package="CellNOptR")
    res<-plotModel(ToyModel, CNOlist=CNOlistToy, compressed=c("TRAF6", "p38"), 
        graphvizParams=list(mode="classic", fontsize=30))
    

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.