## ----v1, include = FALSE------------------------------------------------------ knitr::opts_chunk$set( collapse = TRUE, comment = "#>", eval = TRUE, crop = NULL ) ## ----install, eval=FALSE------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("alevinQC") ## ----v2, message=FALSE-------------------------------------------------------- library(alevinQC) ## ----v3a, eval=FALSE, results='asis'------------------------------------------ # baseDir # |--alevin # | |--featureDump.txt # | |--filtered_cb_frequency.txt # | |--MappedUmi.txt # | |--quants_mat_cols.txt # | |--quants_mat_rows.txt # | |--quants_mat.gz # | |--raw_cb_frequency.txt # | |--whitelist.txt # |--aux_info # | |--meta_info.json # |--cmd_info.json ## ----v3b, eval=FALSE, results='asis'------------------------------------------ # baseDir # |--alevin # | |--featureDump.txt # | |--raw_cb_frequency.txt # | |--whitelist.txt (depending on how alevin was run) # |--aux_info # | |--meta_info.json # | |--alevin_meta_info.json # |--cmd_info.json ## ----v4----------------------------------------------------------------------- baseDir <- system.file("extdata/alevin_example_v0.14", package = "alevinQC") checkAlevinInputFiles(baseDir = baseDir) ## ----v5, message=FALSE, warning=FALSE----------------------------------------- outputDir <- tempdir() alevinQCReport(baseDir = baseDir, sampleId = "testSample", outputFile = "alevinReport.html", outputFormat = "html_document", outputDir = outputDir, forceOverwrite = TRUE) ## ----v7, message=FALSE-------------------------------------------------------- app <- alevinQCShiny(baseDir = baseDir, sampleId = "testSample") ## ----v8, eval=FALSE----------------------------------------------------------- # shiny::runApp(app) ## ----v9----------------------------------------------------------------------- alevin <- readAlevinQC(baseDir = baseDir) ## ----v10---------------------------------------------------------------------- head(alevin$cbTable) ## ----v11---------------------------------------------------------------------- knitr::kable(alevin$summaryTables$fullDataset) knitr::kable(alevin$summaryTables$initialWhitelist) knitr::kable(alevin$summaryTables$finalWhitelist) ## ----v12---------------------------------------------------------------------- knitr::kable(alevin$versionTable) ## ----v13, warning=FALSE------------------------------------------------------- plotAlevinKneeRaw(alevin$cbTable) plotAlevinBarcodeCollapse(alevin$cbTable) plotAlevinQuant(alevin$cbTable) plotAlevinKneeNbrGenes(alevin$cbTable) ## ----v14---------------------------------------------------------------------- sessionInfo()