Compute observation statistic for permutation framework

Usage

.compute_observation(
  x,
  cluster_info,
  correlation_method,
  n_cores,
  test_genes,
  bin_type,
  bin_param,
  w_x,
  w_y,
  use_cm
)

Arguments

x: a named list (of transcript detection coordinates) or SingleCellExperiment or SpatialExperiment or SpatialFeatureExperiment object. If a named list is provided, every list element is a dataframe containing the transcript detection coordinates and column names must include "feature_name" (gene name), "x" (x coordinate), "y" (y coordinate). The list names must match samples in cluster_info.
cluster_info: A dataframe/matrix containing the centroid coordinates, cluster label and sample for each cell.The column names must include "x" (x coordinate), "y" (y coordinate), "cluster" (cluster label) and "sample" (sample). It is strongly recommended to use syntactically valid names for columns clusters and samples. If invalid names are detected, the function make.names will be employed to generate valid names. A message will also be displayed to indicate this change.
correlation_method: A parameter pass to cor, indicating which correlation coefficient is to be computed. One of "pearson" (default), "kendall", or "spearman": can be abbreviated.
n_cores: A positive number specifying number of cores used for parallelizing permutation testing. Default is one core (sequential processing).
test_genes: A vector of strings giving the name of the genes you want to test correlation for.
bin_type: A string indicating which bin shape is to be used for vectorization. One of "square" (default), "rectangle", or "hexagon".
bin_param: A numeric vector indicating the size of the bin. If the bin_type is "square" or "rectangle", this will be a vector of length two giving the numbers of rectangular quadrats in the x and y directions. If the bin_type is "hexagonal", this will be a number giving the side length of hexagons. Positive numbers only.
w_x: a numeric vector of length two specifying the x coordinate limits of enclosing box.
w_y: a numeric vector of length two specifying the y coordinate limits of enclosing box.
use_cm: A boolean value that specifies whether to create spatial vectors for genes using the count matrix and cell coordinates instead of the transcript coordinates when both types of information are available. The default setting is FALSE.

Value

A named list with the following components

obs.stat: A matrix contains the observation statistic for every gene and every cluster. Each row refers to a gene, and each column refers to a cluster
gene_mt: contains the transcript count in each grid. Each row refers to a grid, and each column refers to a gene.