cellCellReport: HTML report of the result of scTensor

In rikenbit/scTensor: Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition

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", assayNames = "counts", thr=100,
    top="full", p=0.05, upper=20,
    goenrich=TRUE, meshenrich=TRUE, reactomeenrich=TRUE,
    doenrich=TRUE, ncgenrich=TRUE, dgnenrich=TRUE, nbins=40)

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").
assayNames	The unit of gene expression for using scTensor (e.g. normcounts, cpm...etc) (Default: "counts").
thr	The threshold for selection of top pecentage of core tensor elements (Default: 100 (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: 20)
goenrich	Whether GO-Enrichment analysis is performed (Default: TRUE)
meshenrich	Whether MeSH-Enrichment analysis is performed (Default: TRUE)
reactomeenrich	Whether Reactome-Enrichment analysis is performed (Default: TRUE)
doenrich	Whether DO-Enrichment analysis is performed (Default: TRUE)
ncgenrich	Whether NCG-Enrichment analysis is performed (Default: TRUE)
dgnenrich	Whether DGN-Enrichment analysis is performed (Default: TRUE)
nbins	The number of bins used for the two dimensional plot of schex (Default: 40)

Value

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

Author(s)

Koki Tsuyuzaki

See Also

SingleCellExperiment.

Examples

	if(interactive()){
	# Package Loading
	library("SingleCellExperiment")
	library("AnnotationHub")
	if(!require(LRBaseDbi)){
	    BiocManager::install("LRBaseDbi")
	    library(LRBaseDbi)
	}
	ah <- AnnotationHub()
	dbfile <- query(ah, c("LRBaseDb", "Homo sapiens", "v002"))[[1]]
	LRBase.Hsa.eg.db <- LRBaseDbi::LRBaseDb(dbfile)

	# Data Loading
	data(GermMale)
	data(labelGermMale)
	data(tsneGermMale)

	# SingleCellExperiment Object
	sce <- SingleCellExperiment(assays=list(counts = GermMale))
	reducedDims(sce) <- SimpleList(TSNE=tsneGermMale$Y)

	# User's Original Normalization Function
	CPMED <- function(input){
	    libsize <- colSums(input)
	    median(libsize) * t(t(input) / libsize)
	}
	# Normalization
	normcounts(sce) <- log10(CPMED(counts(sce)) + 1)

	# Registration of required information into metadata(sce)
	cellCellSetting(sce, LRBase.Hsa.eg.db, names(labelGermMale))

	# Rank Estimation
	rks <- cellCellRanks(sce, assayNames="normcounts")

	# CCI Tensor Decomposition
	set.seed(1234)
	cellCellDecomp(sce, ranks=rks$selected, assayNames="normcounts")

	# HTML Report
	options(device.ask.default = FALSE)
	cellCellReport(sce, reducedDimNames="TSNE",
        out.dir=tempdir(), html.open=FALSE,
        title="The result of scTensor",
        author="The person who runs this script",
        assayNames="counts", thr=100,
        top="full", p=0.05, upper=20,
        goenrich=TRUE, meshenrich=TRUE, reactomeenrich=TRUE,
        doenrich=TRUE, ncgenrich=TRUE, dgnenrich=TRUE, nbins=40)
    }else{
        showMethods("cellCellReport")
    }

rikenbit/scTensor documentation built on Jan. 28, 2023, noon