PathwaySpace (version 1.1.0)

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)