runBanksyUMAP: Run UMAP on a BANKSY embedding.

In prabhakarlab/Banksy: Spatial transcriptomic clustering

Run UMAP on a BANKSY embedding.

Description

Run UMAP on a BANKSY embedding.

Usage

runBanksyUMAP(
  se,
  use_agf = FALSE,
  lambda = 0.2,
  use_pcs = TRUE,
  npcs = 20L,
  dimred = NULL,
  ndims = NULL,
  assay_name = NULL,
  scale = TRUE,
  group = NULL,
  n_neighbors = 30L,
  spread = 3,
  min_dist = 0.1,
  n_epochs = 300L,
  M = NULL,
  seed = NULL,
  ...
)

Arguments

se	A SpatialExperiment, SingleCellExperiment or SummarizedExperiment object with computeBanksy ran.
use_agf	A logical vector specifying whether to use the AGF for computing UMAP.
lambda	A numeric vector in \in [0,1] specifying a spatial weighting parameter. Larger values (e.g. 0.8) incorporate more spatial neighborhood and find spatial domains, while smaller values (e.g. 0.2) perform spatial cell-typing.
use_pcs	A logical scalar specifying whether to run UMAP on PCs. If FALSE, runs on the BANKSY matrix.
npcs	An integer scalar specifying the number of principal components to use if use_pcs is TRUE.
dimred	A string scalar specifying the name of an existing dimensionality reduction result to use. Will overwrite use_pcs if supplied.
ndims	An integer scalar specifying the number of dimensions to use if dimred is supplied.
assay_name	A string scalar specifying the name of the assay used in computeBanksy.
scale	A logical scalar specifying whether to scale features before UMAP. Only used when use_pcs is FALSE. Defaults to TRUE.
group	A string scalar specifying a grouping variable for samples in se. This is used to scale the samples in each group separately.
n_neighbors	An integer scalar specifying the number of neighbors to use for UMAP.
spread	A numeric scalar specifying the effective scale of embedded points.
min_dist	A numeric scalar specifying the effective min. dist. between embedded points.
n_epochs	An integer scalar specifying the number of epochs to run UMAP optimization.
M	Advanced usage. An integer vector specifying the highest azimuthal Fourier harmonic to use. If specified, overwrites the use_agf argument.
seed	Seed for UMAP. If not specified, no seed is set.
...	parameters to pass to uwot::umap

Details

This function runs UMAP on the principal components computed on the BANKSY matrix.

Value

A SpatialExperiment / SingleCellExperiment / SummarizedExperiment object with UMAP coordinates in reducedDims(se).

Examples

data(rings)
spe <- computeBanksy(rings, assay_name = "counts", M = 1, k_geom = c(15, 30))
spe <- runBanksyPCA(spe, M = 1, lambda = 0.2, npcs = 20)
spe <- runBanksyUMAP(spe, M = 1, lambda = 0.2)

prabhakarlab/Banksy documentation built on April 11, 2024, 2:45 p.m.