attractorsToLaTeX: Create LaTeX state table of attractors

In BoolNet: Construction, Simulation and Analysis of Boolean Networks

Create LaTeX state table of attractors

Description

Exports state tables of attractors (corresponding to the plot generated by plotAttractors with mode="table") to a LaTeX document.

Usage

attractorsToLaTeX(attractorInfo, 
                  subset, 
                  title = "", 
                  grouping = list(), 
                  plotFixed = TRUE,
                  onColor = "[gray]{0.9}",
                  offColor = "[gray]{0.6}",
                  reverse = FALSE, 
                  file = "attractors.tex")

Arguments

attractorInfo	An object of class AttractorInfo, as returned by getAttractors, or an object of class SymbolicSimulation, as returned by simulateSymbolicModel.
subset	An subset of attractors to be exported. This is a vector of attractor indices in attractorInfo.
grouping	An optional structure to form groups of genes in the plot. This is a list with the following elements: class A vector of names for the groups. These names will be printed in the region belonging to the group in the table. index A list with the same length as class. Each element is a vector of gene indices belonging to the group.
title	An optional title for the plot
plotFixed	If this is true, genes with fixed values are included in the plot. Otherwise, these genes are not shown.
onColor	An optional color value for the 1/ON values in the table. Defaults to dark grey.
offColor	An optional color value for the 0/OFF values in the table. Defaults to light grey.
reverse	Specifies the order of the genes in the plot. By default, the first gene is placed in the first row of the table. If reverse=TRUE, the first gene in the network is placed in the bottom row of the table.
file	The file to which the LaTeX document is written. Defaults to "attractors.tex".

Details

This function creates LaTeX tables that visualize the states of synchronous attractors. Asynchronous attractors are ignored. Attractors in attractorInfo are first grouped by length. Then, a LaTeX table environment is created for each attractor length (i.e. one plot with all attractors consisting of 1 state, one plot with all attractors consisting of 2 states, etc.). The output file does not contain a document header and requires the inclusion of the packages tabularx and colortbl. The tables have the genes in the rows and the states of the attractors in the columns. If not specified otherwise, cells of the table are light grey for 0/OFF values and dark grey for 1/ON values. If grouping is set, the genes are rearranged according to the indices in the group, horizontal separation lines are plotted between the groups, and the group names are printed.

Value

A list of matrices corresponding to the plots is returned. Each of these matrices has the genes in the rows and the states of the attractors in the columns.

See Also

getAttractors, plotAttractors, sequenceToLaTeX, plotSequence

Examples

## Not run: 
# load example data
data(cellcycle)

# get attractors
attractors <- getAttractors(cellcycle)

# output LaTeX document
attractorsToLaTeX(attractors, file="attractors.tex")

## End(Not run)

BoolNet documentation built on Oct. 2, 2023, 5:08 p.m.