Generate nearest neighbour correlation

This function calculates the nearest neighbour correlation for each feature (eg, proteins) in each sample. This is calculated by taking the correlation between each cell and its nearest neighbours cell for a particular feature. This function supports spatial proteomics, and spatial transcriptomics.

Usage

run_nn_correlation(data, type = "spatial_p", num_top_gene = NULL, ncores = 1)

Arguments

data

A list object containing data matrix and celltype and sample vector.

type

The type of dataset, either "scrna", "spatial_t", or "spatial_p".

num_top_gene

Number of top variable genes to use when genes is not provided. Defaults to 1500.

ncores

Number of cores for parallel processing.

Value

a dataframe of samples x features The features are in the form of protein 1, protein 2 ... etc, with the numbers representing Pearson's correlation.

Examples

utils::data("example_scrnaseq" , package = "scFeatures")
data <- example_scrnaseq[1:50, 1:20]
celltype <- data$celltype 
data <- data@assays$RNA@data
sample <- sample( c("patient1", "patient2", "patient3"), ncol(data) , replace= TRUE )
x <- sample(1:100, ncol(data) , replace = TRUE)
y <- sample(1:100, ncol(data) , replace = TRUE)
spatialCoords <- list( x , y)
alldata <- scFeatures:::formatData(data = data, sample = sample, celltype = celltype, 
spatialCoords  = spatialCoords )
feature_nn_correlation <- run_nn_correlation(
    alldata, type = "spatial_p", ncores = 1
)
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero