calcNhoodDistance {miloR} | R Documentation |
This function will calculate Euclidean distances between single-cells in a
neighbourhood using the same dimensionality as was used to construct the graph.
This step follows the makeNhoods
call to limit the number of distance
calculations required.
calcNhoodDistance(x, d, reduced.dim = NULL, use.assay = "logcounts")
x |
A |
d |
The number of dimensions to use for computing within-neighbourhood
distances. This should be the same value used construct the |
reduced.dim |
If x is an |
use.assay |
A character scalar defining which |
A Milo
object with the distance slots populated.
Mike Morgan, Emma Dann
library(SingleCellExperiment) ux <- matrix(rpois(12000, 5), ncol=200) vx <- log2(ux + 1) pca <- prcomp(t(vx)) sce <- SingleCellExperiment(assays=list(counts=ux, logcounts=vx), reducedDims=SimpleList(PCA=pca$x)) milo <- Milo(sce) milo <- buildGraph(milo, d=30, transposed=TRUE) milo <- makeNhoods(milo) milo <- calcNhoodDistance(milo, d=30) milo