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Run mistyR multiview spatial modeling

Source: R/RunMistyR.R
RunMistyR.Rd

Build a small mistyR view composition from a spatial Seurat object, train MISTy models, collect results, and store a SCOP-style result bundle in srt@tools. The intraview is always created from the selected assay layer; optional juxtaview and paraview components describe local and broader spatial context. mistyR is an optional Bioconductor dependency installable with BiocManager::install("mistyR").

Usage

RunMistyR(
  srt,
  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,
  ...
)

Arguments

srt

A Seurat object.

assay

Assay used for expression. If NULL, the default assay is used.

layer

Assay layer used for expression values.

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. If NULL, the first image is used when present.

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().

juxta_neighbor_thr

Neighbor threshold passed to mistyR::add_juxtaview().

view_cached

Whether generated mistyR views should use cache.

results_folder

Folder passed to mistyR::run_misty(). If NULL, a temporary folder is used.

seed, target_subset, 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 srt@tools. This can be large.

verbose

Whether to print the message. Default is TRUE.

...

Additional named arguments passed to mistyR::run_misty().

Value

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

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial <- Seurat::NormalizeData(spatial, assay = "Spatial", verbose = FALSE)

if (
  isTRUE(check_r("mistyR", verbose = FALSE))
) {
  spatial <- RunMistyR(
    spatial,
    assay = "Spatial",
    layer = "data",
    features = rownames(spatial)[1:10],
    coord.cols = c("x", "y"),
    views = "para",
    para_l = 5,
    cv_folds = 3,
    verbose = FALSE
  )
  spatial@tools$MistyR$summary
}
#> Error in check_r("mistyR", verbose = FALSE): could not find function "check_r"