makeMetaCategorical: Updates shinycell config to recognize a metadata as a...

In SGDDNB/ShinyCell: Shiny Interactive Web Apps for Single-Cell Data

Updates shinycell config to recognize a metadata as a discrete one

Description

Updates shinycell config to recognize a metadata as a discrete one. This function is useful when a discrete metadata only contains integers, e.g. unspervised cluster labels starting from 0 to (n-1) clusters. If these metadata are not factored, then ShinyCell is unable to recognise these as discrete metadata automatically. This is especially important when working with loom files as they do not support factors/levels by default.

Usage

makeMetaCategorical(scConf, meta.to.input, obj, maxLevels = 50)

Arguments

scConf	shinycell config data.table
meta.to.input	metadata from the single-cell metadata to be made discrete. Must match one of the following: Seurat objects: column names in [e-mail] i.e. colnames([e-mail]) 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
obj	input single-cell object for Seurat (v3+) / SingleCellExperiment data or input file path for h5ad / loom files
maxLevels	maximum number of levels allowed for categorical metadata. Metadata with nlevels > maxLevels will throw up an error message

Value

updated shinycell config data.table

Author(s)

John F. Ouyang

Examples

scConf = makeMetaCategorical(scConf, "clusterID", loom_obj)

SGDDNB/ShinyCell documentation built on Jan. 25, 2024, 3:19 p.m.