Plotting correlations on Vissium data in Seurat

Plotting correlations on Vissium data in Seurat

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