Description Usage Arguments Details See Also Examples
Perform geometric transformations of a gate associated with a node of a GatingHierarchy
or
GatingSet
. This method is a wrapper for transform_gate
that enables
updating of the gate associated with a node of a GatingHierarchy
or GatingSet
.
transform_gate
calls gs_pop_set_gate
to modify the provided GatingHierarchy
or GatingSet
directly so there is no need to reassign 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 flowCore::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.
1 2 3 4 5 6 7 8 9 10 11 12 
obj 
A 
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. For 
deg 
An angle in degrees by which the gate should be rotated in the counterclockwise direction. 
rot_center 
A separate 2dimensional center of rotation for the gate, if desired. By default, this will
be the center for 
dx 
Either a numeric scalar or numeric vector. If it is scalar, this is just the desired shift of the gate in
its first dimension. If it is a vector, it specifies both 
dy 
A numeric scalar specifying the desired shift of the gate in its second dimension. 
center 
A numeric vector specifying where the center or centroid should be moved (rather than specifiying 
... 
Assignments made to the slots of the particular Gatetype filter object in the form "<slot_name> = <value>" 
This method allows changes to the four filter types defined by simple geometric gates (quadGate
,
rectangleGate
, ellipsoidGate
, and polygonGate
) using
equally simple geometric transformations (shifting/translation, scaling/dilation, and rotation). The method also
allows for directly resetting the slots of each Gatetype object. 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.
First, transform_gate
will apply any direct alterations to the slots of the supplied Gatetype filter object.
For example, if "mean = c(1,3)
" is present in the argument list when transform_gate
is called on a
ellipsoidGate
object, the first change applied will be to shift the mean
slot to (1,3)
. The method
will carry over the dimension names from the gate, so there is no need to provide column or row names with arguments
such as mean
or cov
for ellipsoidGate
or boundaries
for polygonGate
.
transform_gate
then passes the geometric arguments (dx
, dy
, deg
, rot_center
, scale
,
and center
) to the methods which perform each respective type of transformation:
shift_gate
, scale_gate
, or rotate_gate
.
The order of operations is to first scale, then rotate, then shift. The default behavior of each operation follows
that of its corresponding method but for the most part these are what the user would expect. A few quick notes:
rotate_gate
is not defined for rectangleGate
or quadGate
objects, due to their definition as
having 1dimensional boundaries.
The default center for both rotation and scaling of a polygonGate
is the centroid of the polygon. This
results in the sort of scaling most users expect, with a uniform scale factor not distorting the shape of the original polygon.
1 2 3 4 5 6 7 8  ## Not run:
# Scale the original gate nonuniformly, rotate it 15 degrees, and shift it
transform_gate(gs, node, scale = c(2,3), deg = 15, dx = 500, dy = 700)
# Scale the original gate (in this case an ellipsoidGate) after moving its center to (1500, 2000)
transform_gate(gs, node, scale = c(2,3), mean = c(1500, 2000))
## End(Not run)

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