Accessor Functions for PathwaySpace Objects

Get or set vertex signals, decay functions, and the active feature in a PathwaySpace object.

vertexSignal() gets or sets the numeric signal assigned to each vertex, used as input for spatial projection.

vertexDecay() gets or sets the decay function assigned to each vertex, controlling how the signal attenuates with distance.

activeFeature() gets or sets the active feature name, which automatically extracts the corresponding signal from the fdata slot or node attributes and assigns it to vertexSignal().

Usage

# S4 method for class 'PathwaySpace'
vertexSignal(x)

# S4 method for class 'PathwaySpace'
vertexSignal(x) <- value

# S4 method for class 'PathwaySpace'
vertexDecay(x)

# S4 method for class 'PathwaySpace'
vertexDecay(x) <- value

# S4 method for class 'PathwaySpace'
activeFeature(x)

# S4 method for class 'PathwaySpace'
activeFeature(x) <- value

Arguments

x

A PathwaySpace class object.

value

The new value to assign:

• For vertexSignal(): a numeric vector or scalar.

• For vertexDecay(): a decay function or list of decay functions (see linearDecay, weibullDecay).

• For activeFeature(): a single string matching a feature name (see gs_features) or a node attribute (see gs_names).

Value

The updated PathwaySpace object.

Examples

library(PathwaySpace)

# Load a demo igraph
data('gtoy1', package = 'RGraphSpace')
ps <- buildPathwaySpace(gtoy1, nrc = 100)
#> Validating arguments...
#> Validating the 'igraph' object...
#> Normalizing node coordinates to graph space...
#> Creating a 'PathwaySpace' object...

# Check vertex names
names(ps)
#> [1] "n1" "n2" "n3" "n4" "n5"

##--------------------------------------
## 'vertexSignal' accessor

# Access signal values from all vertices
vertexSignal(ps)
#> n1 n2 n3 n4 n5 
#>  0  0  0  0  0 

# Modify signal value of a specific vertex
vertexSignal(ps)[1] <- 1

# Modify signal value of specific vertices
vertexSignal(ps)[c("n2","n3")] <- 1

# Set '1s' to all vertices
vertexSignal(ps) <- 1

##--------------------------------------
## 'activeFeature' accessor

# Assign a signal feature matrix
signal_mtx <- matrix(
  rep(rnorm(gs_vcount(ps)), 2),
  ncol = 2,
  dimnames = list(names(ps), c("feature1", "feature2"))
)
gs_fdata(ps) <- signal_mtx

# Set the active feature — automatically updates vertexSignal()
activeFeature(ps) <- "feature1"
#> Setting active feature 'feature1' from feature matrix...

##--------------------------------------
## 'vertexDecay' accessor

# Access decay function of a specific vertex
vertexDecay(ps)[["n3"]]
#> function (x, signal) 
#> {
#>     y <- signal * 0.001^((x/0.15)^1.05)
#>     return(y)
#> }
#> <environment: 0x5f3a431e3d30>
#> attr(,"name")
#> [1] "weibullDecay"

# Modify decay function of a specific vertex
vertexDecay(ps)[["n3"]] <- linearDecay()

# Modify decay functions of two vertices
vertexDecay(ps)[c("n1","n3")] <- list( weibullDecay() )

# Modify decay functions of all vertices
vertexDecay(ps) <- weibullDecay(shape = 2)