Run mistyR multiview spatial modeling

Model feature expression using MISTy intraview and spatial predictors. Juxtaview and paraview predictors describe local and broader neighborhoods.

Usage

RunMistyR(
  object,
  assay = NULL,
  layer = "data",
  features = NULL,
  image = NULL,
  coord.cols = c("col", "row"),
  views = "para",
  para_l = 10,
  para_zoi = 0,
  para_family = c("gaussian", "exponential", "linear", "constant"),
  para_approx = 1,
  para_nn = NULL,
  juxta_neighbor_thr = 15,
  view_cached = FALSE,
  results_folder = NULL,
  seed = 42,
  target_subset = NULL,
  bypass_intra = FALSE,
  cv_folds = 10,
  model_cached = FALSE,
  append = FALSE,
  tool_name = "MistyR",
  store_results = TRUE,
  store_views = FALSE,
  verbose = TRUE,
  coordinate_space = c("raw", "legacy_display"),
  sample.by = NULL,
  ...,
  srt = NULL
)

Arguments

object: A Seurat object.
assay: Assay used for expression. If NULL, the default assay is used.
layer: Assay layer used for expression values. Values must be finite; missing or infinite values are rejected rather than replaced by zero.
features: Features used by MISTy. If NULL, variable features are used when available; otherwise all assay features are used.
image: Name of the Seurat spatial image. Required when multiple images are present; a single image is selected automatically when NULL.
coord.cols: Metadata coordinate columns used when no Seurat image coordinates are available.
views: Spatial views to add besides the required intraview. One or both of "para" and "juxta".
para_l, para_zoi, para_family, para_approx, para_nn: Parameters passed to mistyR::add_paraview(). para_l and para_zoi use the selected coordinate units; para_nn is a unitless neighbor count.
juxta_neighbor_thr: Neighbor threshold passed to mistyR::add_juxtaview(), expressed in the selected coordinate units.
view_cached: Whether generated mistyR views should use cache.
results_folder: Folder passed to mistyR::run_misty(). If NULL, a temporary folder is used.
target_subset: Original feature names or numeric indices of selected features to model. Character names are mapped to the internal MISTy names.
seed, bypass_intra, cv_folds, model_cached, append: Parameters passed to mistyR::run_misty().
tool_name: Name used to store results in srt@tools.
store_results: Whether to store results in srt@tools.
store_views: Whether to store the mistyR view composition in object@tools. This can be large.
verbose: Whether to print the message. Default is TRUE.
coordinate_space: Coordinate system used to build MISTy views. The default is raw acquisition coordinates; "legacy_display" remains an explicit compatibility option.
sample.by: Optional metadata column identifying independent samples. The selected cells must belong to one sample. Split independent samples into separate runs; when NULL, the caller is responsible for supplying one spatial coordinate field.
...: Additional named arguments passed to mistyR::run_misty().
srt: Deprecated alias for object; supply exactly one of the two. It will be removed in scop 1.0.0.

Value

A Seurat object with results stored in srt@tools[[tool_name]] when store_results = TRUE.

Examples

if (FALSE) { # \dontrun{
data(visium_human_pancreas_sub)
spatial <- Seurat::NormalizeData(visium_human_pancreas_sub, verbose = FALSE)
# Paraview bandwidth: 1000 full-resolution image pixels.
spatial <- RunMistyR(
  spatial,
  assay = "Spatial", features = rownames(spatial)[1:5],
  image = "slice1", views = "para", para_l = 1000,
  cv_folds = 3, verbose = FALSE
)
MistyRPlot(spatial, type = "improvements", top_n = 5)
} # }