## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", error = FALSE, warning = FALSE, message = FALSE, crop = NULL ) stopifnot(requireNamespace("htmltools")) htmltools::tagList(rmarkdown::html_dependency_font_awesome()) ## ---- echo=FALSE, out.width='50%', fig.align='center'------------------------- knitr::include_graphics(path = system.file(package="iSEE", "www/iSEE.png", mustWork=TRUE)) ## ----library------------------------------------------------------------------ library(iSEE) ## ----demostart, eval=FALSE---------------------------------------------------- # iSEE(se) ## ----quickstart, eval=FALSE--------------------------------------------------- # example(iSEE, ask=FALSE) ## ----allen-dataset------------------------------------------------------------ library(scRNAseq) sce <- ReprocessedAllenData(assays = "tophat_counts") # specifying the assays to speed up the example sce ## ----colData_sce-------------------------------------------------------------- colnames(colData(sce)) ## ----------------------------------------------------------------------------- library(scater) sce <- logNormCounts(sce, exprs_values="tophat_counts") ## ----allen-dataset-2---------------------------------------------------------- sce <- runPCA(sce) sce <- runTSNE(sce) reducedDimNames(sce) ## ----------------------------------------------------------------------------- rowData(sce)$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()