## ----setup, include = FALSE------------------------------------------------ knitr::opts_chunk$set( collapse = TRUE, comment = "#>", error = FALSE, warning = FALSE, message = FALSE ) stopifnot(requireNamespace("htmltools")) htmltools::tagList(rmarkdown::html_dependency_font_awesome()) ## ----library--------------------------------------------------------------- library(iSEE) ## ----allen-dataset--------------------------------------------------------- library(scRNAseq) data(allen) allen ## ----colData_sce----------------------------------------------------------- colnames(colData(allen)) ## -------------------------------------------------------------------------- library(scater) sce <- as(allen, "SingleCellExperiment") counts(sce) <- assay(sce, "tophat_counts") sce <- normalize(sce) ## ----allen-dataset-2------------------------------------------------------- sce <- runPCA(sce) sce <- runTSNE(sce) reducedDimNames(sce) ## -------------------------------------------------------------------------- rowData(sce)$mean_log <- rowMeans(logcounts(sce)) rowData(sce)$var_log <- apply(logcounts(sce), 1, var) ## ---- echo=FALSE, results="hide"------------------------------------------- # Saving and reloading so we don't have to run it again later. # This requires that NO OTHER VIGNETTE is alphabetically ordered before this one. saveRDS(file="sce.rds", sce) ## ----allen-dataset-4------------------------------------------------------- app <- iSEE(sce) ## ----runApp, eval=FALSE---------------------------------------------------- # shiny::runApp(app) ## ----citation-------------------------------------------------------------- citation("iSEE") ## ----sessioninfo----------------------------------------------------------- sessionInfo() # devtools::session_info()