correlationSpot: Plotting correlations on Vissium data in Seurat

In zktuong/ktplots: Plot single-cell data dotplots

Plotting correlations on Vissium data in Seurat

Description

Plotting correlations on Vissium data in Seurat

Usage

correlationSpot(
  st,
  genes = NULL,
  celltypes = NULL,
  geneset = NULL,
  mode = c("high", "low", "both"),
  cutoff = 0.5,
  standardize = TRUE,
  dims = 1:30,
  k.params = 10,
  resolution = 1,
  rna_slot = "SCT",
  label_slot = "predictions",
  by = c("image", "expression"),
  average_by_cluster = FALSE,
  ...
)

Arguments

st	spatial transcriptomics data in Seurat.
genes	gene or genes of interest for performing correlations. Must exist as row name(s) in the 'rna_slot'.
celltypes	celltype or celltypes of interest for performing correlations. Must exist as row name(s) in the 'label_slot'.
geneset	geneset or column in meta.data for performing correlations. Must exist as column name(s) in the meta.data.
mode	whether or not to restrict the output to just high expressing values, low expressing values or both. Caveat with using both is low expressing ~ low expressing will still return a high correlation value.
cutoff	percentile cut off for determining mode output.
standardize	whether or not to scale values from 0 to 1 before performing correlations.
dims	number of dimensions used for calculating neighborhoods in spatial data.
k.params	number of k neighbors for calculating neighborhoods in spatial data.
resolution	resolution of spatial clustering.
rna_slot	name of gene expression slot. Defaults to 'SCT'.
label_slot	name of label/prediction slot. Defaults to 'predictions'.
by	whether or not to define spatial clusters based on image spatial location or gene expression.
average_by_cluster	whether or not to return the output averaged across clusters.
...	passed to Seurat::SpatialFeaturePlot

Value

SpatialFeaturePlot

zktuong/ktplots documentation built on April 12, 2025, 9:53 p.m.