Plot a sequence of states
Visualizes sequences of states in synchronous Boolean networks, either by drawing a table of the involved states in two colors, or by drawing a graph of transitions between the successive states.
plotSequence(network, startState, includeAttractorStates = c("all","first","none"), sequence, title = "", mode=c("table","graph"), plotFixed = TRUE, grouping = list(), onColor="#4daf4a", offColor = "#e41a1c", layout, drawLabels=TRUE, drawLegend=TRUE, highlightAttractor=TRUE, reverse = FALSE, borderColor = "black", eps=0.1, attractor.sep.lwd = 2, attractor.sep.col = "blue", ...)
network: An object of class BooleanNetwork or SymbolicBooleanNetwork for which a sequence of state transitions is calculated
startState: The start state of the sequence
includeAttractorStates: Specifies whether the actual attractor states are included in the plot or not (see also getPathToAttractor). If includeAttractorStates = "all" (which is the default behaviour), the sequence ends when the attractor was traversed once. If includeAttractorStates = "first", only the first state of attractor is added to the sequence. If includeAttractorStates = "none", the sequence ends with the last non-attractor state.
sequence: The alternative call to plotSequence requires the specification of the sequence itself instead of the network and the start state. The sequence must be provided as a data frame with the genes in the columns and the successive states in the rows. For example, sequences can be obtained using getPathToAttractor or getAttractorSequence (however, the specialized plot plotAttractors exists for attractors).
title: An optional title for the plot
mode: Switches between two kinds of attractor plots. See Details for more information. Default is "table".
plotFixed: This optional parameter is only used if mode="table". If this is true, genes with fixed values are included in the plot. Otherwise, these genes are not drawn.
grouping: This optional parameter is only used if mode="table" and specifies a structure to form groups of genes in the plot. This is a list with the following elements:
class. Each element is a vector of gene names or gene indices belonging to the group.onColor: This optional parameter is only used if mode="table" and specifies the color value for the 1/ON values in the table. Defaults to green.
offColor: This optional parameter is only used if mode="table" and specifies the color value for the 0/OFF values in the table. Defaults to red.
layout: If mode="graph", this parameter specifies a layouting function that determines the placement of the nodes in the graph. Please refer to the layout manual entry in the igraph package for further details. By default, the nodes are placed in a horizontal line.
drawLabels: This parameter is only relevant if mode="graph". It determines whether the nodes of the graph are annotated with the corresponding values of the genes in the attractor states.
drawLegend: Specifies whether a color key for the ON/OFF states is drawn if mode="table". Defaults to TRUE.
highlightAttractor: If set to true, the attractor states are highlighted in the plot. If mode="table", a line is drawn at the begin of the attractor, and the states are labeled correspondingly. If mode="graph", the attractor transitions are drawn as bold lines. Information on the attractor must be supplied in the attribute attractor of the sequence, which is a vector of indices of the states that belong to the attractor. This attribute is usually present if the sequence was obtained using getPathToAttractor.
reverse: Specifies the order of the genes in the plot. By default, the first gene is placed in the first row of the plot. If reverse=TRUE (which was the default until BoolNet version 2.0.2), the first gene in the network is placed in the bottom row of the plot.
borderColor: Specifies the border or seprating color of states in an attractor. Defaults to "black".
eps: Specifies plotting margin for the sequence of states. Defaults to 0.1.
attractor.sep.lwd: Specifies the line width of the attractor separator. Defaults to 2.
attractor.sep.col: Specifies the line color of the attractor separator. Defaults to "blue".
...: Further graphical parameters to be passed to plot.igraph if mode="graph".
This function comprises two different types of plots:
The "table" mode visualizes the gene values of the states in the sequence. The figure is a table with the genes in the rows and the successive states of the sequence in the columns. Cells of the table are (by default) red for 0/OFF values and green 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.
The "graph" mode visualizes the transitions between different states. It creates a graph in which the vertices are the states in the sequence and the edges are state transitions among these states.
The function can be called with different types of inputs: The user can specify the parameters network, startState and includeAttractorStates), in which case getPathToAttractor is called to obtain the sequence. Alternatively, the sequence can be supplied directly as a data frame in the sequence parameter.
If mode="table", a matrix corresponding to the table is returned. The matrix has the genes in the rows and the states of the attractors in the columns. If sequence was supplied, this corresponds to the transposed input whose rows may be rearranged if grouping was set.
If mode="graph", an object of class igraph describing the graph for the sequence is returned.
sequenceToLaTeX, plotAttractors, attractorsToLaTeX, getPathToAttractor, getAttractorSequence, simulateSymbolicModel
## Not run: # load example data data(cellcycle) # alternative 1: supply network and start state # and plot sequence as a table plotSequence(network=cellcycle, startState=rep(1,10), includeAttractorStates="all") # alternative 2: calculate sequence in advance sequence <- getPathToAttractor(cellcycle, state=rep(1,10), includeAttractorStates="all") # plot sequence as a graph plotSequence(sequence=sequence, mode="graph") ## End(Not run)
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