reportTGIF: Function for reporting the result of 'calcTGIF' function

In rikenbit/scTGIF: Cell type annotation for unannotated single-cell RNA-Seq data

Function for reporting the result of calcTGIF function

Description

calcTGIF function calculates what kind of cellular patterns and functional patterns are contained in single-cell RNA-seq data and reportTGIF function generates report of analytic result.

Usage

reportTGIF(sce, out.dir=tempdir(), html.open=FALSE,
    title="The result of scTGIF",
    author="The person who runs this script",
    assayNames="counts")

Arguments

sce	A object generated by instantization of SingleCellExperiment-class.
out.dir	Output directory user want to save the report (Default: tempdir()).
html.open	Whether html is opened when reportTGIF is finished (Default: FALSE)
title	Title of report (Default: "The result of scTGIF")
author	The name of user name (Default: "The person who runs this script")
assayNames	The unit of gene expression for using scTGIF (e.g. normcounts, cpm...etc) (Default: "counts").

Value

Some file is generated to output directory user specified.

Author(s)

NA

Examples

    if(interactive()){
        # Package loading
        library("SingleCellExperiment")
        library("GSEABase")
        library("msigdbr")

        # Test data
        data("DistalLungEpithelium")
        data("pca.DistalLungEpithelium")
        data("label.DistalLungEpithelium")

        # Test data
        par(ask=FALSE)
        plot(pca.DistalLungEpithelium, col=label.DistalLungEpithelium, pch=16,
            main="Distal lung epithelium dataset", xlab="PCA1",
            ylab="PCA2", bty="n")
        text(0.1, 0.05, "AT1", col="#FF7F00", cex=2)
        text(0.07, -0.15, "AT2", col="#E41A1C", cex=2)
        text(0.13, -0.04, "BP", col="#A65628", cex=2)
        text(0.125, -0.15, "Clara", col="#377EB8", cex=2)
        text(0.09, -0.2, "Cilliated", col="#4DAF4A", cex=2)

        # Load the gmt file from MSigDB
        # Only "Entrez Gene ID" can be used in scTGIF
        # e.g. gmt <- GSEABase::getGmt(
        #     "/PATH/YOU/SAVED/THE/GMTFILES/h.all.v6.0.entrez.gmt")
        # Here we use msigdbr to retrieve mouse gene sets

        # Mouse gene set (NCBI Gene ID)
        m_df <- msigdbr(species = "Mus musculus", category = "H")[,
            c("gs_name", "entrez_gene")]

        # Convert to GeneSetCollection
        hallmark = unique(m_df$gs_name)
        gsc <- lapply(hallmark, function(h){
            target = which(m_df$gs_name == h)
            geneIds = unique(as.character(m_df$entrez_gene[target]))
            GeneSet(setName=h, geneIds)
        })
        gmt <- GeneSetCollection(gsc)

        # SingleCellExperiment-class
        sce <- SingleCellExperiment(
            assays = list(counts = DistalLungEpithelium))
        reducedDims(sce) <- SimpleList(PCA=pca.DistalLungEpithelium)

        # 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)
        settingTGIF(sce, gmt, reducedDimNames="PCA",
            assayNames="normcounts")

        # Functional Annotation based on jNMF
        calcTGIF(sce, ndim=7)

        # HTML Reprt
        reportTGIF(sce,
            html.open=TRUE,
            title="scTGIF Report for DistalLungEpithelium dataset",
            author="Koki Tsuyuzaki")
    }

rikenbit/scTGIF documentation built on Jan. 14, 2023, 4:18 a.m.