spatialPatterns: Automatic expression histology in *SpatialDE*

In sales-lab/spatialDE: R wrapper for SpatialDE

Automatic expression histology in SpatialDE

Description

Group spatially variable genes into spatial patterns using Automatic Expression Histology, using the SpatialDE Python package.

Usage

spatialPatterns(x, de_results, ...)

## S4 method for signature 'matrix'
spatialPatterns(
  x,
  de_results,
  coordinates,
  qval_thresh = 0.05,
  n_patterns,
  length,
  verbose = FALSE
)

## S4 method for signature 'SpatialExperiment'
spatialPatterns(
  x,
  de_results,
  qval_thresh = 0.05,
  n_patterns,
  length,
  assay_type = "counts",
  verbose = FALSE
)

Arguments

x	A numeric matrix of counts where genes are rows and cells are columns. Alternatively, a SpatialExperiment object.
de_results	data.frame resulting from run() or spatialDE().
...	For the generic, arguments to pass to specific methods.
coordinates	A data.frame with sample coordinates. Each row is a sample, the columns with coordinates should be named 'x' and 'y'. For the SpatialExperiment method, coordinates are taken from spatialCoords(x).
qval_thresh	numeric scalar, specifying the q-value significance threshold to filter de_results. Only rows in de_results with qval < qval_thresh will be kept. To disable, set qval_thresh = NULL.
n_patterns	integer The number of spatial patterns
length	numeric The characteristic length scale of the clusters
verbose	A logical controlling the display of a progress bar from the Python package.
assay_type	A character string specifying the assay from x to use as input. Defaults to "counts".

Value

A list of two data.frames (pattern_results, patterns):

• pattern_results: data.frame with pattern membership information for each gene.

• patterns the posterior mean underlying expression from genes in given spatial patterns.

Author(s)

Davide Corso, Milan Malfait, Lambda Moses

References

Svensson, V., Teichmann, S. & Stegle, O. SpatialDE: identification of spatially variable genes. Nat Methods 15, 343–346 (2018). https://doi.org/10.1038/nmeth.4636

SpatialDE 1.1.3: the version of the Python package used under the hood.

See Also

The individual steps performed by this function: stabilize(), regress_out() and spatial_patterns().

Examples

## Mock up a SpatialExperiment object wit 100 cells and 3 genes
set.seed(42)
spe <- mockSVG(size = 10, tot_genes = 3, de_genes = 1, return_SPE = TRUE)

## Run spatialDE
de_results <- spatialDE(spe)

spatial_patterns <- spatialPatterns(spe, de_results = de_results,
    qval_thresh = NULL, n_patterns = 4L, length = 1.5,
    verbose = FALSE
)

head(spatial_patterns$pattern_results)
head(spatial_patterns$patterns)

sales-lab/spatialDE documentation built on Feb. 12, 2024, 2:47 p.m.