CAESAR.coembedding.image: Compute Co-embedding with Image Information Using CAESAR

In CAESAR.Suite: CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation

Compute Co-embedding with Image Information Using CAESAR

Description

This function performs co-embedding of both cells and genes using the CAESAR method. It integrates spatial transcriptomics data from a Seurat object ('seu') with image features ('feature_img') and a spatial adjacency matrix to compute the low-dimensional co-embedding.

Usage

CAESAR.coembedding.image(
  seu,
  feature_img,
  pos,
  reduction.name = "caesar",
  q = 50,
  lower.med = 3.5,
  upper.med = 5.5,
  radius.upper = 400,
  q.image = 10,
  weighted = FALSE,
  approx_Phi = TRUE,
  seed = 1,
  ...
)

Arguments

seu	A Seurat object containing spatial transcriptomics data.
feature_img	A matrix representing features extracted from a histology image using a Visual Transformer. Rows correspond to spots and columns represent image features. The row names of 'feature_img' should match the column names of 'seu'.
pos	A matrix of spatial coordinates for the spots (e.g., spatial positions of cells or pixels in the image). The row names of 'pos' should match the column names of 'seu'.
reduction.name	A character string specifying the name of the dimensional reduction method to store in the Seurat object. Default is "caesar".
q	An integer specifying the number of dimensions for the reduced co-embeddings. Default is 50.
lower.med	A numeric value specifying the lower bound for the desired median number of neighbors in the spatial adjacency matrix. Default is 3.5.
upper.med	A numeric value specifying the upper bound for the desired median number of neighbors in the spatial adjacency matrix. Default is 5.5.
radius.upper	A numeric value specifying the upper limit of the search radius for the spatial adjacency matrix. Default is 400.
q.image	An integer specifying the number of dimensions for the reduced image embeddings. Default is 10.
weighted	Logical, indicating whether to apply weighted PCA on the image features. Default is FALSE.
approx_Phi	Logical, indicating whether to use an approximate method for Phi matrix estimation. Default is TRUE.
seed	An integer used to set the random seed for reproducibility. Default is 1.
...	Additional arguments passed to 'cellembedding_image_seurat'.

Value

The modified Seurat object with the computed cell and gene embeddings stored in the specified reduction slot.

See Also

cellembedding_image_seurat for computing cell embeddings. add.gene.embedding for adding gene embeddings to a Seurat object.

Examples

data(toydata)

seu <- toydata$seu
pos <- toydata$pos
imgf <- toydata$imgf

seu <- CAESAR.coembedding.image(seu, imgf, pos)
print(seu)

CAESAR.Suite documentation built on April 3, 2025, 10:32 p.m.