recommend_k: function of iSpatial

In Czh3/iSpatial: infer transcriptome-wide spatial expression via integration of scRNA and spRNA

function of iSpatial

Description

recommand optimized K value for KNN

Usage

recommend_k(
  spRNA,
  scRNA,
  dims = 1:30,
  k.neighbor = c(5, seq(10, 80, by = 10)),
  infered.assay = "enhanced",
  n.core = 8,
  correct.spRNA = FALSE,
  correct.scRNA = FALSE,
  correct.weight.NN = 0.2,
  correct.neighbor = 5
)

Arguments

spRNA	seurat object of spatial transcriptome data
scRNA	seurat object of single cell RNA-seq data
dims	which dimensions to use when find the nearest neighbors
k.neighbor	a list of K to test
infered.assay	names of output assay in seurat object
n.core	number of CPU cores used to parallel.
correct.spRNA	Whether to stabilize expression in spRNA.
correct.scRNA	Whether to stabilize expression in scRNA.
correct.neighbor	number of nearest neighbors used to correct expr.
weighted.KNN	we use a dynamics weight to assign scRNA values to spRNA. The dynamics weight based on the correlation between scRNA cell and spRNA cell.
RNA.weight	the weight of scRNA-seq expression when genes detected both in spRNA and scRNA. RNA.weight should be 0 to 1. The inferred expression = (1 - RNA.weight) * spRNA + RNA.weight * scRNA.

Value

returns a ggplot2 object.

Czh3/iSpatial documentation built on Sept. 15, 2022, 10:32 p.m.