Run Giotto nearest-network clustering

Run Giotto as a temporary backend for nearest-network clustering and return the complete Giotto object together with extracted cluster results. The input Seurat object is not modified.

Usage

RunGiottoCluster(
  srt,
  assay = NULL,
  layer = "data",
  features = NULL,
  image = NULL,
  coord.cols = c("x", "y"),
  method = c("leiden", "louvain"),
  dims = 1:20,
  k = 20,
  resolution = 1,
  cluster_colname = "Giotto_cluster",
  tool_name = "GiottoCluster",
  store_giotto = TRUE,
  conversion_params = list(),
  preprocess_params = list(),
  network_params = list(),
  cluster_params = list(),
  verbose = TRUE,
  seed = 11
)

Arguments

srt

A Seurat object.

assay

Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.

layer

Assay layer used as the expression matrix.

features

Features used for PCA and clustering. If NULL, current variable features are used, falling back to all assay features.

image

Name of the Seurat spatial image used by the spatial workflow. If NULL, the first image is used when present.

coord.cols

Metadata coordinate columns used by the spatial workflow when no image is available.

method

Giotto clustering method.

dims

Dimensions used to build the Giotto nearest-neighbor network.

k

Number of nearest neighbors used by Giotto.

resolution

Resolution passed to Giotto clustering.

cluster_colname

Result column name recorded in returned parameters. This function does not write to srt@meta.data.

tool_name

Result name recorded in returned parameters. This function does not write to srt@tools.

store_giotto

Deprecated compatibility argument. The complete Giotto object is always returned in the giotto element.

conversion_params

Additional parameters passed to Giotto::createGiottoObject().

preprocess_params

Additional parameters passed to Giotto::runPCA().

network_params

Additional parameters passed to Giotto::createNearestNetwork().

cluster_params

Additional parameters passed to Giotto clustering.

verbose

Whether to print the message. Default is TRUE.

seed

Random seed for reproducibility. Default is 11.

Value

A giotto2_result list containing the full Giotto object, cluster assignments, Giotto metadata, parameters, features, and cells.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
giotto_clusters <- list(
  clusters = data.frame(
    cluster = paste0("cluster_", (seq_len(ncol(spatial)) - 1) %% 3 + 1),
    row.names = colnames(spatial)
  ),
  parameters = list(
    cluster_colname = "Giotto_cluster",
    coord.cols = c("x", "y"),
    k = 8,
    resolution = 0.4
  )
)
class(giotto_clusters) <- c("giotto2_cluster", "giotto2_result", "list")
head(giotto_clusters$clusters)
#>                      cluster
#> TGGTATCGGTCTGTAT-1 cluster_1
#> ATTATCTCGACAGATC-1 cluster_2
#> TGAGATCAAATACTCA-1 cluster_3
#> CTGGTCCTAACTTGGC-1 cluster_1
#> ATAGTCTTTGACGTGC-1 cluster_2
#> GGGTGGTCCAGCCTGT-1 cluster_3
GiottoPlot(
  giotto_clusters,
  srt = spatial,
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)


if (
  isTRUE(check_r("giotto-suite/Giotto", verbose = FALSE))
) {
spatial <- Seurat::NormalizeData(spatial, assay = "Spatial", verbose = FALSE)
spatial <- Seurat::FindVariableFeatures(
  spatial,
  assay = "Spatial",
  nfeatures = 300,
  verbose = FALSE
)
giotto_clusters <- RunGiottoCluster(
  spatial,
  assay = "Spatial",
  layer = "data",
  dims = 1:10,
  k = 8,
  resolution = 0.4,
  coord.cols = c("x", "y")
)

head(giotto_clusters$clusters)
}
#> Error in check_r("giotto-suite/Giotto", verbose = FALSE): could not find function "check_r"