PathwaySpace (version 1.5.1)

expDecay: Constructor of exponential decay functions

Description

The expDecay() constructor either creates a decay function or returns a ggplot object for visualizing the decay model. It is a utility function used internally by circularProjection and polarProjection.

Usage

expDecay(decay = 0.001, pdist = 0.15, plot = FALSE, demo.signal = 1)

Value

Returns either a function of the form function(x, signal) { ... } or, if plot = TRUE, a ggplot

object illustrating the decay model.

Arguments

decay

A decay factor (in [0,1]). This term indicates how much a signal decreases as a function of distance in pathway space. For example, at a specific distance defined by the pdist parameter, the signal intensity will be the initial signal multiplied by decay.

pdist

A distance normalization term (in (0, 1]) at which the signal reaches signal * decay. This parameter is used to anchor the decay to a meaningful distance (see details). Also, when pdist = 1, it will represent the diameter of the inscribed circle within the coordinate space of a PathwaySpace object.

plot

A logical value indicating whether to return a ggplot object.

demo.signal

A numeric value in [-Inf, Inf], only passed when plot = TRUE to visualize the decay curve with a specific signal intensity. The value is ignored by the function constructor, as the decay function itself is returned without using an initial signal.

Author

Sysbiolab Team

Details

The expDecay() constructor creates an exponential decay model. It describes how a signal decreases as a function of distance, controlled by a decay rate parameter.

The decay function is defined as:

$$y = signal \times decay^{\left(\frac{x}{pdist}\right)}$$

where \(signal\) represents the initial intensity, \(decay\) controls the rate of attenuation, and \(x\) is a vector of normalized distances. The \(pdist\) parameter anchors the model such that:

• \(y = signal\) when \(x = 0\)

• \(y = signal \times decay\) when \(x = pdist\)

See Also

linearDecay, weibullDecay

Examples

# Return a decay function
decay_fun <- expDecay(decay = 0.25, pdist = 0.5)

# Plot decay model parameters
# expDecay(decay = 0.25, pdist = 0.5, plot = TRUE)