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",
  suppress_warnings = TRUE,
  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
suppress_warnings: boolean to suppress the warning when running Seurat::RunUMAP
verbose: non-negative integer
...: extra arguments to Seurat::RunUMAP

Value

a DimReduc SeuratObject