Build a SpatialDWLS Signature

Constructs a DWLS signature matrix from single-cell data using Giotto and a marker-selection strategy: either compute markers with a supported method (scran, gini, mast) or pass a custom vector of marker genes directly.

Usage

build_model_spatial_dwls(
  single_cell_obj,
  assay_sc = "counts",
  marker_method = "scran",
  topNgenes = 100,
  cell_type_col = "cell_ontology_class",
  dim_method = "pca",
  cluster_method = "leiden",
  ...
)

Arguments

single_cell_obj

SingleCellExperiment with cell type annotations.

assay_sc

Single-cell assay to use.

marker_method

Marker genes or method to compute markers (scran, gini, or mast).

topNgenes

Number of top-ranked marker genes per cluster.

cell_type_col

Column containing cell type labels.

dim_method

Dimension reduction method for Giotto workflow: pca, tsne, or umap.

cluster_method

Clustering method for Giotto workflow: leiden, louvain, kmeans, or hclust.

...

Additional parameters passed to Giotto helpers.