cellCellReport {scTensor}R Documentation

HTML report of the result of scTensor

Description

The result is saved as HTML report which contains with multiple files.

Usage

cellCellReport(sce, reducedDimNames,
    out.dir=tempdir(), html.open=FALSE,
    title="The result of scTensor",
    author="The person who runs this script", thr=40, top="full", p=0.05, upper=100)

Arguments

sce

A object generated by instantization of SingleCellExperiment-class.

reducedDimNames

The name of two-dimentional data saved in reducedDimNames slot of SingleCellExperiment object.

out.dir

The output directory for saving HTML report (out.dir: tempdir()).

html.open

Whether the result of HTML report is opened when the calculation is finished (Default: FALSE).

title

The title of HTML report (Default: "The result of scTensor").

author

The author of HTML report (Default: "The person who runs this script").

thr

The threshold for selection of top pecentage of core tensor elements (Default: 40 (1 to 100)).

top

top genes in each (*,*,*)-pattern which are selected and summarized in the report (Default: "full")

p

The threshold of p-value of the enrichment analysis (Default: 1E-2)

upper

The maxium number of HTML reports generates (Default: 100)

Value

The result is saved as HTML report which contains with multiple files.

Author(s)

Koki Tsuyuzaki

See Also

SingleCellExperiment.

Examples

	if(interactive()){
	library("SingleCellExperiment")
	library("LRBase.Hsa.eg.db")
	library("MeSH.Hsa.eg.db")

	data(GermMale)
	data(labelGermMale)
	data(tsneGermMale)
	sce <- SingleCellExperiment(assays=list(counts = GermMale))
	reducedDims(sce) <- SimpleList(TSNE=tsneGermMale$Y)
	cellCellSetting(sce, LRBase.Hsa.eg.db, labelGermMale, names(labelGermMale))
	rks <- cellCellRanks(sce)
	cellCellDecomp(sce, ranks=rks$selected)
	cellCellReport(sce, reducedDimNames="TSNE",
	    title="Cell-cell interaction within Germline_Male, GSE86146",
	    author="Koki Tsuyuzaki", thr=30, html.open=TRUE)
    }

[Package scTensor version 1.0.3 Index]