circularProjection,PathwaySpace-method: Circular Projection of Graph-Associated Signals

Description

circularProjection() implements a convolution algorithm to project vertex-associated signals onto a 2D image space using a circular decay function.

Usage

# S4 method for PathwaySpace
circularProjection(
  ps,
  feature = activeFeature(ps),
  decay.fun = weibullDecay(),
  aggregate.fun = signalAggregation(),
  k = gs_vcount(ps),
  rescale = TRUE,
  verbose = TRUE,
  pdist = deprecated()
)

Value

A preprocessed PathwaySpace class object.

Arguments

ps: A PathwaySpace class object.
feature: A single string specifying the feature to project as a signal. Must match either a feature name (see gs_features(ps)) or a node attribute (see gs_names(ps)). If a node attribute, make sure it is of numeric type. If the signal does not come from internal features, assign it directly using the vertexSignal accessor.
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).
k: A single positive integer specifying the maximum number of vertices whose signals contribute to the projection. Defaults to gs_vcount(ps), i.e. all vertices are considered. Specifically, at each point in space, the k-top decayed signals are retained prior to aggregation. Reducing k focuses the projection on the strongest local signals, filtering out weaker contributions.
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).
pdist: Deprecated as of PathwaySpace 1.0.2; this parameter is now passed internally through decay.fun.

Author

Sysbiolab Team

Examples

Run this code

library(PathwaySpace)

# Load a demo igraph
data('gtoy1', package = 'RGraphSpace')

# Create a new PathwaySpace object
ps <- buildPathwaySpace(gtoy1, nrc = 100)
# note: adjust 'nrc' to increase image resolution

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

# Create a 2D-landscape image
ps <- circularProjection(ps)