reportTGIF {scTGIF} | R Documentation

## 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")
        }

[Package scTGIF version 1.4.0 Index]