Create a shinycell config data.table containing (i) the single-cell metadata to display on the Shiny app, (ii) ordering of factors / categories of categorical metadata and (iii) colour palettes associated with each metadata.
create_config(obj, meta.to.include = NA, legendCols = 4, maxLevels = 50)input single-cell object for Seurat (v3+) / SingleCellExperiment data or input file path for h5ad / loom files
columns to include from the single-cell metadata.
Default is NA, which is to use all columns. Users can specify
the columns to include, which must match one of the following:
Seurat objects: column names in seu@meta.data
i.e. colnames(seu@meta.data)
SCE objects: column names in sce@colData
i.e. colnames(sce@colData)
h5ad files: column names in h5ad.obs
i.e. h5ad.obs.columns.values
loom files: column names in loom/col_attrs
i.e. loom/col_attrs.names
maximum number of columns allowed when displaying the legends of categorical metadata
maximum number of levels allowed for categorical metadata. Metadata with nlevels > maxLevels will be discarded automatically
shinycell config data.table
if (FALSE) {
scConf = create_config(obj)
}