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Create a CellSight config data.table

Source: R/createConfig.R
createConfig.Rd

Create a CellSight 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.

Usage

createConfig(obj, meta.to.include = NA, legendCols = 4, maxLevels = 50)

Arguments

obj

input Seurat (v3+) object or input file path for h5ad file

meta.to.include

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)

  • h5ad files: column names in h5ad.obs i.e. h5ad.obs.columns.values

legendCols

maximum number of columns allowed when displaying the legends of categorical metadata

maxLevels

maximum number of levels allowed for categorical metadata. Metadata with nlevels > maxLevels will be discarded automatically

Value

CellSight config data.table

Author

John F. Ouyang

Examples

if (FALSE) { # \dontrun{
scConf = createConfig(obj)
} # }