% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/clustering.R

\name{getProfileNeighbors}

\alias{getProfileNeighbors}

\title{Get profile specific neighbors}

\usage{

getProfileNeighbors(

  object,

  assay = NULL,

  method = "kNN",

  k = 10,

  data.type = "pca",

  dims = seq_len(30),

  graph.key = method

)

}

\arguments{

\item{object}{a VoltRon object}

\item{assay}{assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. 

if NULL, the default assay will be used, see \link{vrMainAssay}.}

\item{method}{the method used for graph construction, SNN or kNN}

\item{k}{number of neighbors for kNN}

\item{data.type}{the type of embedding used for neighborhood calculation, e.g. raw counts (raw), normalized counts (norm), PCA embeddings (pca), UMAP embeddings (umap) etc.}

\item{dims}{the set of dimensions of the embedding data}

\item{graph.key}{the name of the graph}

}

\description{

Get neighbors of spatial points

}