## ----testdata, echo=TRUE, message=FALSE--------------------------------------- library("scTGIF") library("SingleCellExperiment") library("GSEABase") library("msigdbr") data("DistalLungEpithelium") data("pca.DistalLungEpithelium") data("label.DistalLungEpithelium") ## ----testdata2, echo=TRUE, fig.width=7, fig.height=7-------------------------- 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) ## ----gmt, echo=TRUE----------------------------------------------------------- m_df = msigdbr(species = "Mus musculus", category = "H")[, c("gs_name", "entrez_gene")] 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) gmt = gmt[1:10] # Reduced for this demo ## ----setting, echo=TRUE------------------------------------------------------- sce <- SingleCellExperiment(assays = list(counts = DistalLungEpithelium)) reducedDims(sce) <- SimpleList(PCA=pca.DistalLungEpithelium) ## ----setting2, echo=TRUE------------------------------------------------------ CPMED <- function(input){ libsize <- colSums(input) median(libsize) * t(t(input) / libsize) } normcounts(sce) <- log10(CPMED(counts(sce)) + 1) ## ----setting3, echo=TRUE------------------------------------------------------ settingTGIF(sce, gmt, reducedDimNames="PCA", assayNames="normcounts") ## ----calc, echo=TRUE---------------------------------------------------------- calcTGIF(sce, ndim=3) ## ---- report, echo=TRUE------------------------------------------------------- reportTGIF(sce, html.open=FALSE, title="scTGIF Report for DistalLungEpithelium dataset", author="Koki Tsuyuzaki") ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()