In csoneson/alevinQC: Generate QC Reports For Alevin Output

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Introduction

The purpose of the r Biocpkg("alevinQC") package is to generate a summary QC report based on the output of an alevin [@Srivastava2019-fz] run. The QC report can be generated as a html or pdf file, or launched as a shiny application.

Installation

alevinQC can be installed using the BiocManager CRAN package.

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

After installation, load the package into the R session.

library(alevinQC)

Note that in order to process output from Salmon v0.14 or later, you need Alevin v1.1 or later.

Assumed output directory structure

For more information about running alevin, we refer to the documentation. When invoked, alevin generates several output files in the specified output directory. r Biocpkg("alevinQC") assumes that this structure is retained, and will return an error if it isn't - thus, it is not recommended to move or rename the output files from alevin. r Biocpkg("alevinQC") assumes that the following files (in the indicated structure) are available in the provided baseDir (note that currently, in order to generate the full set of files, alevin must be invoked with the --dumpFeatures flag).

For alevin versions before 0.14:

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

For alevin version 0.14 and later:

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

Check that all required alevin files are available

The report generation functions (see below) will check that all the required files are available in the provided base directory. However, you can also call the function checkAlevinInputFiles() to run the check manually. If one or more files are missing, the function will raise an error indicating the missing file(s).

baseDir <- system.file("extdata/alevin_example_v0.14", package = "alevinQC")
checkAlevinInputFiles(baseDir = baseDir)

Generate QC report

The alevinQCReport() function generates the QC report from the alevin output. Depending on the file extension of the outputFile argument, and the value of outputFormat, the function can generate either an html report or a pdf report.

outputDir <- tempdir()
alevinQCReport(baseDir = baseDir, sampleId = "testSample", 
               outputFile = "alevinReport.html", 
               outputFormat = "html_document",
               outputDir = outputDir, forceOverwrite = TRUE)

Create shiny app

In addition to static reports, r Biocpkg("alevinQC") can also generate a shiny application, containing the same summary figures as the pdf and html reports.

app <- alevinQCShiny(baseDir = baseDir, sampleId = "testSample")

Once created, the app can be launched using the runApp() function from the r CRANpkg("shiny") package.

shiny::runApp(app)

It is possible to export the data used internally by the interactive application (in effect, the output from the internal call to readAlevinQC() or readAlevinFryQC()). To enable such export, first generate the app object as in the example above, and then assign the call to shiny::runApp() to a variable to capture the output. For example:

if (interactive()) {
    out <- shiny::runApp(app)
}

To activate the export, make sure to click the button 'Close app' in the top right corner in order to close the application (don't just close the window). This will take you back to your R session, where the variable out will be populated with the data used in the app.

Generate individual plots

The individual plots included in the QC reports can also be independently generated. To do so, we must first read the alevin output into an R object.

alevin <- readAlevinQC(baseDir = baseDir)

The resulting list contains four entries:

• cbTable: a data.frame with various inferred characteristics of the individual cell barcodes.
• summaryTables: a list of data.frames with summary information about the full data set, the initial set of whitelisted cells and the final set of whitelisted cells, respectively.
• versionTable: a matrix with information about the invokation of alevin.
• type: a character scalar indicating how alevinQC interpreted the alevin output directory.

head(alevin$cbTable)

knitr::kable(alevin$summaryTables$fullDataset)
knitr::kable(alevin$summaryTables$initialWhitelist)
knitr::kable(alevin$summaryTables$finalWhitelist)

knitr::kable(alevin$versionTable)

The plots can now be generated using the dedicated plotting functions provided with r Biocpkg("alevinQC") (see the help file for the respective function for more information).

plotAlevinKneeRaw(alevin$cbTable)
plotAlevinBarcodeCollapse(alevin$cbTable)
plotAlevinQuant(alevin$cbTable)
plotAlevinKneeNbrGenes(alevin$cbTable)

Session info

sessionInfo()

References

csoneson/alevinQC documentation built on Dec. 25, 2024, 8:18 p.m.