## ----v1, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = TRUE
)

## ----install, eval=FALSE---------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("alevinQC")

## ----v2, message=FALSE-----------------------------------------------------
library(alevinQC)

## ----v3, 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

## ----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()