scale_gate: Simplified geometric scaling of gates associated with nodes

In RGLab/flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Simplified geometric scaling of gates associated with nodes

Description

Scale a gate associated with a node of a GatingHierarchy or GatingSet. This method is a wrapper for scale_gate that enables updating of the gate associated with a node of a GatingHierarchy or GatingSet.

scale_gate calls gs_pop_set_gate to modify the provided GatingHierarchy or GatingSet directly so there is no need to re-assign its output. The arguments will be essentially identical to the flowCore method, except for the specification of the target gate. Rather than being called on an object of type filter, here it is called on a GatingHierarchy or GatingSet object with an additional character argument for specifying the node whose gate should be transformed. The rest of the details below are taken from the flowCore documentation.

Usage

## S3 method for class 'GatingHierarchy'
scale_gate(obj, y, scale = NULL, ...)

Arguments

obj	A GatingHierarchy or GatingSet object
y	A character specifying the node whose gate should be modified
scale	Either a numeric scalar (for uniform scaling in all dimensions) or numeric vector specifying the factor by which each dimension of the gate should be expanded (absolute value > 1) or contracted (absolute value < 1). Negative values will result in a reflection in that dimension.
...	not used

Details

This method allows uniform or non-uniform geometric scaling of filter types defined by simple geometric gates (quadGate, rectangleGate, ellipsoidGate, and polygonGate) Note that these methods are for manually altering the geometric definition of a gate. To easily transform the definition of a gate with an accompanyging scale transformation applied to its underlying data, see ?ggcyto::rescale_gate.

The scale argument passed to scale_gate should be either a scalar or a vector of the same length as the number of dimensions of the gate. If it is scalar, all dimensions will be multiplicatively scaled uniformly by the scalar factor provided. If it is a vector, each dimension will be scaled by its corresponding entry in the vector.

The scaling behavior of scale_gate depends on the type of gate passed to it. For rectangleGate and quadGate objects, this amounts to simply scaling the values of the 1-dimensional boundaries. For polygonGate objects, the values of scale will be used to determine scale factors in the direction of each of the 2 dimensions of the gate (scale_gate is not yet defined for higher-dimensional polytopeGate objects). Important: For ellipsoidGate objects, scale determines scale factors for the major and minor axes of the ellipse, in that order. Scaling by a negative factor will result in a reflection in the corresponding dimension.

See Also

transform_gate flowCore::scale_gate

Examples

## Not run: 
# Scales both dimensions by a factor of 5
scale_gate(gs, node, 5)

# Shrinks the gate in the first dimension by factor of 1/2
# and expands it in the other dimension by factor of 3
scale_gate(gs, node, c(0.5,3))

## End(Not run)

RGLab/flowWorkspace documentation built on March 17, 2024, 2:24 p.m.