Create Seurat dimension reduction objects of Tilted-CCA

Create Seurat dimension reduction objects of Tilted-CCA

Usage

create_SeuratDim(
  input_obj,
  what,
  aligned_umap_assay = NULL,
  scale_max_1 = NULL,
  scale_max_2 = NULL,
  seurat_obj = NULL,
  seurat_assay = "RNA",
  verbose = 0,
  ...
)

Arguments

input_obj

a multiSVD object that is the output of tiltedCCA_decomposition

what

a character, either "common", "distinct_1", or "distinct_2" for which embedding to construct the visualization for

aligned_umap_assay

either NULL or a UMAP assay in seurat_assay (in which case the resulting UMAP will be rotated to best mimic the relative orientation of cells in seurat_obj[[aligned_umap_assay]])

scale_max_1

numeric or NULL, to threshold Modality 1 in magnitude prior to computing latent dimensions

scale_max_2

numeric or NULL, to threshold Modality 2 in magnitude prior to computing latent dimensions

seurat_obj

the Seurat object that was used to compute input_obj, the multiSVD_obj

seurat_assay

the assay in seurat_obj to assign the resulting embedding to

verbose

non-negative integer

...

Value

a DimReduc

SeuratObject