SFE-transform: Affine transfortaion of SFE object in histological space

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Affine transfortaion of SFE object in histological space

Description

These functions perform affine transformations on SFE objects, including all geometries and images. The transformation is performed on each sample as a whole. This differs from functions such as mirrorImg in that mirrorImg and rotateImg transform the image with the center at the center of the image itself. In contrast, the center of transformation here is the center of the bounding box of the entire sample, including images.

Usage

transpose(sfe, sample_id = "all", maxcell = NULL, filename = "")

mirror(
  sfe,
  sample_id = "all",
  direction = c("vertical", "horizontal"),
  maxcell = NULL,
  filename = ""
)

rotate(sfe, sample_id = "all", degrees, maxcell = 1e+07)

translate(sfe, sample_id = "all", v)

scale(sfe, sample_id = "all", factor)

affine(sfe, sample_id = "all", M, v, maxcell = 1e+07)

Arguments

sfe	An SFE object.
sample_id	Sample(s) to transform.
maxcell	Rotating SpatRasterImage will convert it into ExtImage, loading the image into memory. This argument specifies the maximum number of pixels in the image loaded into memory. The image will be down sampled to approximately this number of pixels.
filename	character. Output filename
direction	character. Should (partially) match "vertical" to flip by rows, or "horizontal" to flip by columns
degrees	How many degrees to rotate. Positive number means clockwise and negative number means counterclockwise.
v	Vector to spatially translate the SFE object.
factor	Numeric, scaling factor.
M	A 2x2 numeric matrix for the linear transformation in the xy plane.

Details

For images that are not loaded into memory, rotateImg will load SpatRasterImage into memory and all image operations except translate will load BioFormatsImage into memory.

Value

An SFE object with the sample(s) transformed.

Examples

library(SFEData)
sfe <- McKellarMuscleData("small")
sfe2 <- transpose(sfe)
sfe3 <- mirror(sfe)

pachterlab/SpatialFeatureExperiment documentation built on Dec. 20, 2024, 3:41 a.m.