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Polar Projection of Graph-Associated Signals

Source: R/pspaceMethods.R
polarProjection-methods.Rd

polarProjection implements a convolution algorithm to project signals across a 2D-coordinate system.

Usage

# S4 method for class 'PathwaySpace'
polarProjection(
  ps,
  k = 2,
  beta = 10,
  decay.fun = weibullDecay(pdist = 1),
  aggregate.fun = signalAggregation(),
  polar.fun = polarDecay(),
  directional = FALSE,
  edge.norm = TRUE,
  rescale = TRUE,
  verbose = TRUE,
  theta = deprecated(),
  pdist = deprecated()
)

Arguments

ps

A PathwaySpace class object.

k

A single positive integer determining the k-top signals for the convolution operation.

beta

An exponent (in [0, +Inf)) used in the polar projection functions (see polarDecay). It controls the shape of the polar projection by modulating the angular span. For example, \(beta = 0\) yields a circular projection, \(beta = 1\) produces a cardioid-like shape, and beta > 1 progressively narrows the projection along a reference edge axis.

decay.fun

A signal decay function. Available options include 'Weibull', 'exponential', and 'linear' (see weibullDecay). Users may also define a custom decay model with at least two arguments, e.g., function(x, signal) { ... }, which should returns a vector of projected signals of the same length as x. Additional arguments may include any variable available as a graph vertex attribute.

aggregate.fun

A function used to aggregate the projected signals. It must be provided as a unary function, e.g., function(x) { ... }, which should aggregate a vector of signals to a scalar value. Available options include 'mean', 'wmean', 'log.wmean', and 'exp.wmean' (See signalAggregation).

polar.fun

A polar decay function (see polarDecay).

directional

If directional edges are available, this argument can be used to orientate the signal projection on directed graphs.

edge.norm

Scale distances based on edge lengths (when edge.norm=TRUE) or based on full coordinate space (when edge.norm=FALSE).

rescale

A logical value indicating whether to rescale the signal. If the signal >=0, then it will be rescaled to [0, 1]; if the signal <=0, then it will be rescaled to [-1, 0]; and if the signal in (-Inf, +Inf), then it will be rescaled to [-1, 1].

verbose

A logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

theta

Deprecated as of PathwaySpace 1.0.2; use 'beta' instead.

pdist

Deprecated as of PathwaySpace 1.0.2; this parameter is now passed internally through decay.fun.

Value

A preprocessed PathwaySpace class object.

See also

buildPathwaySpace

Author

Sysbiolab Team

Examples

# Load a demo igraph
data('gtoy2', package = 'RGraphSpace')

# Create a new PathwaySpace object
ps <- buildPathwaySpace(gtoy2, nrc = 100)
#> Validating arguments...
#> Validating the 'igraph' object...
#> Normalizing node coordinates to graph space...
#> Creating a 'PathwaySpace' object...
# note: adjust 'nrc' to increase image resolution

# Set '1s' as vertex signal
vertexSignal(ps) <- 1

# Set edge weight
# gs_edge_attr(ps, "weight") <- c(-1, 1, 1, 1, 1, 1)

# Create a 2D-landscape image
ps <- polarProjection(ps, pdist=1)
#> Validating arguments...
#> Using polar projection on undirected graph...
#> Mapping 'x' and 'y' coordinates...
#> Computing linear and angular distances...
#> Running signal convolution...