cellCellSetting: Parameter setting for scTensor

Description Usage Arguments Value Author(s) See Also Examples

Description

All parameters is saved to metadata slot of SingleCellExperiment object.

Usage

1
cellCellSetting(sce, lrbase, label, lr.evidence="known", color=NULL)

Arguments

sce

A object generated by instantization of SingleCellExperiment-class.

lrbase

Ligand-Receptor database (LRBase.XXX.eg.db-type package).

label

Cellular label information for distingusishing which cells belong to common celltypes.

lr.evidence

The evidence code for L-R pair list (Default: "known"). When you specify "known", DLRP, IUPHAR, HPMR, CELLPHONEDB, SINGLECELLSIGNALR are searched, and other databases are searched, when you specify "putative". You can also specify multiple databases at once (e.g. c("SWISSPROT_STRING", "TREMBL_STRING")). cf. https://github.com/rikenbit/lrbase-workflow

color

Color scheme for adding color against the cells (Default: NULL). If the value is not specified, automatically the color vector is generated.

Value

The result is saved to metadata slot of SingleCellExperiment object.

Author(s)

Koki Tsuyuzaki

See Also

SingleCellExperiment.

Examples

1
showMethods("cellCellSetting")

rikenbit/scTensor documentation built on Dec. 16, 2021, 5:51 p.m.