spatialAutoCor: Spatial autocorrelation

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Spatial autocorrelation

Description

Find spatial autocorrelation. Note that spatialAutoCorGlobal will return values as a data.table instead of appending information to the gobject. spatialAutoCorLocal will append the results as a spatial enrichment object by default.
If providing external data using either the node_values and/or weight_matrix params, the order of values provided should be the same as the ordering of the columns and rows of the weight matrix.

Usage

spatialAutoCorGlobal(
  gobject = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  feats = NULL,
  method = c("moran", "geary"),
  data_to_use = c("expression", "cell_meta"),
  expression_values = c("normalized", "scaled", "custom"),
  meta_cols = NULL,
  spatial_network_to_use = "kNN_network",
  wm_method = c("distance", "adjacency"),
  wm_name = "spat_weights",
  node_values = NULL,
  weight_matrix = NULL,
  test_method = c("none", "monte_carlo"),
  mc_nsim = 99,
  cor_name = NULL,
  return_gobject = FALSE,
  verbose = TRUE
)

spatialAutoCorLocal(
  gobject = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  feats = NULL,
  method = c("moran", "gi", "gi*", "mean"),
  data_to_use = c("expression", "cell_meta"),
  expression_values = c("normalized", "scaled", "custom"),
  meta_cols = NULL,
  spatial_network_to_use = "kNN_network",
  wm_method = c("distance", "adjacency"),
  wm_name = "spat_weights",
  node_values = NULL,
  weight_matrix = NULL,
  test_method = c("none"),
  enrich_name = NULL,
  return_gobject = TRUE,
  output = c("spatEnrObj", "data.table"),
  verbose = TRUE
)

Arguments

gobject	giotto object
spat_unit	spatial unit
feat_type	feature type
feats	features (expression) on which to run autocorrelation. (leaving as NULL means that all features will be tested)
method	method of autocorrelation. See details (default = 'moran')
data_to_use	if using data from gobject, whether to test using expression ('expression') or cell metadata ('cell_meta')
expression_values	name of expression information to use
meta_cols	columns in cell metadata to test
spatial_network_to_use	spatial network to use
wm_method	type of weight matrix to generate from spatial network if no weight matrix is found attached to the spatial network
wm_name	name of attached weight matrix to use
node_values	alternative method of directly supplying a set of node values
weight_matrix	alternative method of directly supplying a spatial weight matrix
test_method	method to test values for significance (default is no testing)
mc_nsim	when test_method = 'monte_carlo' this is number of simulations to perform
cor_name	name to assign the results in global autocorrelation output
return_gobject	(default = FALSE) whether to return results appended to
verbose	be verbose
enrich_name	name to assign local autocorrelation spatial enrichment results
output	'spatEnrObj' or 'data.table' metadata in the giotto object or as a data.table

Details

Global Methods:

• Moran's I 'moran'

• Geary's C 'geary'

Local Methods:

• Local Moran's I 'moran'

• Getis-Ord Gi 'Gi'

• Getis-Ord Gi* 'Gi*'

• Local mean 'mean'

Functions

• spatialAutoCorGlobal(): Global autocorrelation (single value returned)

• spatialAutoCorLocal(): Local autocorrelation (values generated for each spatial ID)

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.