RunBanksy: Run Banksy on a Seurat Object

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

Run Banksy on a Seurat Object

Description

Run Banksy on a Seurat Object

Usage

RunBanksy(
  object,
  lambda,
  assay = "RNA",
  slot = "data",
  use_agf = FALSE,
  dimx = NULL,
  dimy = NULL,
  dimz = NULL,
  ndim = 2,
  features = "variable",
  group = NULL,
  split.scale = TRUE,
  k_geom = 15,
  n = 2,
  sigma = 1.5,
  alpha = 0.05,
  k_spatial = 10,
  spatial_mode = "kNN_median",
  assay_name = "BANKSY",
  M = NULL,
  verbose = TRUE
)

Arguments

object	A Seurat object
lambda	(numeric) Spatial weight parameter
assay	(character) Assay in Seurat object to use
slot	(character) Slot in Seurat assay to use
use_agf	(boolean) Whether to use the AGF
dimx	(character) Column name of spatial x dimension (must be in metadata)
dimy	(character) Column name of spatial y dimension (must be in metadata)
dimz	(character) Column name of spatial z dimension (must be in metadata)
ndim	(integer) Number of spatial dimensions to extract
features	(character) Features to compute. Can be 'all', 'variable' or a vector of feature names
group	(character) Column name of a grouping variable (must be in metadata)
split.scale	(boolean) Whether to separate scaling by group
k_geom	(numeric) kNN parameter - number of neighbors to use
n	(numeric) kNN_rn parameter - exponent of radius
sigma	(numeric) rNN parameter - standard deviation of Gaussian kernel
alpha	(numeric) rNN parameter - determines radius used
k_spatial	(numeric) rNN parameter - number of neighbors to use
spatial_mode	(character) Kernel for neighborhood computation kNN_median: k-nearest neighbors with median-scaled Gaussian kernel kNN_r: k-nearest neighbors with $1/r$ kernel kNN_rn: k-nearest neighbors with $1/r^n$ kernel kNN_rank: k-nearest neighbors with rank Gaussian kernel kNN_unif: k-nearest neighbors wth uniform kernel rNN_gauss: radial nearest neighbors with Gaussian kernel
assay_name	(character) Name for Banksy assay in Seurat object
M	(numeric) Advanced usage. Highest azimuthal harmonic
verbose	(boolean) Print messages

Value

A Seurat object with new assay holding a Banksy matrix

Author(s)

Joseph Lee, Vipul Singhal

References

Vipul Singhal, Nigel Chou et. al. BANKSY: A Spatial Omics Algorithm that Unifies Cell Type Clustering and Tissue Domain Segmentation

See Also

ComputeBanksy

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.