Affine transformations

Apply an affine transformation matrix to a spatial object. Currently only works for 2D transforms.

Usage

# S4 method for class 'giotto,matrix'
affine(
  x,
  y,
  inv = FALSE,
  spat_unit = ":all:",
  feat_type = ":all:",
  images = ":all:",
  ...
)

# S4 method for class 'missing,missing'
affine(x)

# S4 method for class 'ANY,missing'
affine(x)

# S4 method for class 'ANY,affine2d'
affine(x, y, ...)

# S4 method for class 'SpatVector,matrix'
affine(x, y, inv = FALSE, ...)

# S4 method for class 'giottoPoints,matrix'
affine(x, y, inv = FALSE, ...)

# S4 method for class 'giottoPolygon,matrix'
affine(x, y, inv = FALSE, ...)

# S4 method for class 'spatLocsObj,matrix'
affine(x, y, inv = FALSE, ...)

# S4 method for class 'giottoLargeImage,matrix'
affine(x, y, inv = FALSE, ...)

# S4 method for class 'giottoAffineImage,matrix'
affine(x, y, inv = FALSE, ...)

# S4 method for class 'affine2d,matrix'
affine(x, y, inv = FALSE, ...)

Arguments

x

object to affine transform or a matrix

y

matrix or coercible to matrix (such as affine2d). Should be a matrix with either 2 or 3 columns (linear or affine).

inv

logical. Whether the inverse of the affine transform should be applied.

spat_unit

character vector. spatial units to affect. The :all: token to affect all can be used.

feat_type

character vector. feature types to affect. The :all: token to affect all can be used.

images

character vector. Images to affect. The :all: token to affect all can be used.

...

additional args to pass (none implemented)

Value

affine transformed object or an affine2d if a matrix was passed to x

Examples

m <- diag(rep(1, 3))
trans_m <- matrix(c(1, 0, 0, 0, 1, 0, 200, 300, 1), nrow = 3)
scale_m <- matrix(c(2, 0, 0, 0, 3, 0, 0, 0, 1), nrow = 3)
aff_m <- matrix(c(2, 3, 0, 0.2, 3, 0, 100, 29, 1), nrow = 3)

gpoints <- GiottoData::loadSubObjectMini("giottoPoints")
gpoly <- GiottoData::loadSubObjectMini("giottoPolygon")
sl <- GiottoData::loadSubObjectMini("spatLocsObj")

# creation of affine2d
aff <- affine(m)
aff <- spin(flip(shear(aff, fx = 0.2)), 45)
plot(aff) # blue is start, red is end


# giottoPoints ##############################################
plot(gpoints)

plot(affine(gpoints, trans_m))


# giottoPolygon #############################################
plot(gpoly)

plot(affine(gpoly, scale_m))

plot(affine(gpoly, aff)) # affine() with `affine2d`


# spatLocsObj ###############################################
plot(affine(sl, m))

plot(affine(sl, trans_m))

plot(affine(sl, scale_m))

# this transformation can be inverted
aff_sl <- affine(sl, aff_m)
plot(aff_sl)

plot(affine(aff_sl, aff_m, inv = TRUE))