> ## Documentation Index
> Fetch the complete documentation index at: https://mintlify.com/satijalab/seurat-wrappers/llms.txt
> Use this file to discover all available pages before exploring further.

# RunBanksy()

> Spatial transcriptomics clustering incorporating neighborhood gene expression context

`RunBanksy()` computes a BANKSY matrix that augments each cell's expression with the average expression of its spatial neighbors. The resulting matrix enables clustering that captures both cell type identity and spatial tissue domains.

## Syntax

```r theme={null}
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
)
```

## Parameters

<ParamField path="object" type="Seurat" required>
  A Seurat object with spatial coordinate metadata.
</ParamField>

<ParamField path="lambda" type="numeric" required>
  Spatial weight parameter. `0` uses only cell-intrinsic expression (equivalent to standard clustering). `1` uses only neighborhood expression. Values around `0.2` typically give good cell-type results; `0.8` is better for tissue domain segmentation.
</ParamField>

<ParamField path="assay" type="character" default="RNA">
  Assay in the Seurat object to use.
</ParamField>

<ParamField path="slot" type="character" default="data">
  Slot within the assay to use.
</ParamField>

<ParamField path="use_agf" type="logical" default="FALSE">
  Whether to use the Azimuthal Gabor Filter (AGF) for higher-order neighborhood features.
</ParamField>

<ParamField path="dimx" type="character" default="NULL">
  Column name in cell metadata containing the spatial x-coordinate.
</ParamField>

<ParamField path="dimy" type="character" default="NULL">
  Column name in cell metadata containing the spatial y-coordinate.
</ParamField>

<ParamField path="dimz" type="character" default="NULL">
  Column name in cell metadata containing the spatial z-coordinate (3D data only).
</ParamField>

<ParamField path="ndim" type="integer" default="2">
  Number of spatial dimensions to use (2 or 3).
</ParamField>

<ParamField path="features" type="character" default="variable">
  Features to compute. One of `"all"`, `"variable"`, or a character vector of feature names.
</ParamField>

<ParamField path="group" type="character" default="NULL">
  Column name of a grouping variable in metadata. Used to compute neighbors within groups.
</ParamField>

<ParamField path="split.scale" type="logical" default="TRUE">
  Whether to scale expression separately by group.
</ParamField>

<ParamField path="k_geom" type="numeric" default="15">
  Number of neighbors for the kNN spatial graph (used with kNN-based `spatial_mode`).
</ParamField>

<ParamField path="n" type="numeric" default="2">
  Exponent of radius for `kNN_rn` spatial mode.
</ParamField>

<ParamField path="sigma" type="numeric" default="1.5">
  Standard deviation of the Gaussian kernel for `rNN_gauss` mode.
</ParamField>

<ParamField path="alpha" type="numeric" default="0.05">
  Determines the radius used in `rNN_gauss` mode.
</ParamField>

<ParamField path="k_spatial" type="numeric" default="10">
  Number of neighbors for radial nearest neighbor modes.
</ParamField>

<ParamField path="spatial_mode" type="character" default="kNN_median">
  Kernel for spatial neighborhood computation. Options:

  * `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 with uniform kernel
  * `rNN_gauss` — radial nearest neighbors with Gaussian kernel
</ParamField>

<ParamField path="assay_name" type="character" default="BANKSY">
  Name for the new BANKSY assay stored in the Seurat object.
</ParamField>

<ParamField path="M" type="numeric" default="NULL">
  Highest azimuthal harmonic for AGF computation. Advanced usage.
</ParamField>

<ParamField path="verbose" type="logical" default="TRUE">
  Print progress messages.
</ParamField>

## Returns

A Seurat object with a new assay (default name `BANKSY`) containing the BANKSY-augmented expression matrix. Downstream analysis (PCA, UMAP, clustering) should be run on this assay.

## Examples

```r theme={null}
library(SeuratWrappers)

# Run BANKSY with spatial coordinates in metadata
object <- RunBanksy(
  object = seurat_obj,
  lambda = 0.2,
  assay = "RNA",
  slot = "data",
  dimx = "x",
  dimy = "y",
  features = "variable",
  spatial_mode = "kNN_median",
  k_geom = 15
)

# Downstream clustering on BANKSY assay
DefaultAssay(object) <- "BANKSY"
object <- ScaleData(object)
object <- RunPCA(object)
object <- FindNeighbors(object)
object <- FindClusters(object, resolution = 0.5)
```

## See Also

* [BANKSY method guide](/methods/banksy)