`transform_gate.Rd`

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 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 `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.

# S3 method for GatingHierarchy transform_gate( obj, y, scale = NULL, deg = NULL, rot_center = NULL, dx = NULL, dy = NULL, center = NULL, ... )

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 counter-clockwise direction. |

rot_center | A separate 2-dimensional 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 Gate-type 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 re-setting the slots of each Gate-type 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 Gate-type 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 1-dimensional 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.

if (FALSE) { # Scale the original gate non-uniformly, 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)) }