qcShiny: Generate alevin/alevin-fry summary shiny app

In csoneson/alevinQC: Generate QC Reports For Alevin Output

Generate alevin/alevin-fry summary shiny app

Description

Generate a shiny app summarizing the main aspects of an alevin/alevin-fry quantification run. The app generation assumes that alevin has been run with the –dumpFeatures flag to generate the necessary output files.

Usage

alevinQCShiny(baseDir, sampleId, customCBList = list())

alevinFryQCShiny(mapDir, permitDir, quantDir, sampleId)

simpleafQCShiny(simpleafQuantDir, sampleId)

Arguments

baseDir	(Only used for alevin output) Path to the output directory from the alevin run (should be the directory containing the alevin directory).
sampleId	Sample ID, will be used set the title for the app.
customCBList	Named list with custom set(s) of barcodes to provide summary statistics/plots for, in addition to the whitelists generated by alevin.
mapDir	(Only used for alevin-fry output) Path to the output directory from the salmon alevin run (should be the directory containing the map.rad file).
permitDir	(Only used for alevin-fry output) Path to the output directory from the permit list generation step (should be the directory containing the all_freq.tsv file).
quantDir	(Only used for alevin-fry output) Path to the output directory from the alevin-fry quantification step (should be the directory containing the alevin directory).
simpleafQuantDir	(Only used for simpleaf output) Path to the output directory from the simpleaf run (should be the directory containing the af_map and af_quant directories).

Value

A shiny app.

Author(s)

Charlotte Soneson

Examples

app <- alevinQCShiny(
    baseDir = system.file("extdata/alevin_example_v0.14",
                          package = "alevinQC"),
    sampleId = "example")
if (interactive()) {
    shiny::runApp(app)
}

app <- alevinFryQCShiny(
    mapDir = system.file("extdata/alevinfry_example_v0.5.0/map",
                         package = "alevinQC"),
    permitDir = system.file("extdata/alevinfry_example_v0.5.0/permit",
                            package = "alevinQC"),
    quantDir = system.file("extdata/alevinfry_example_v0.5.0/quant",
                           package = "alevinQC"),
    sampleId = "example")
if (interactive()) {
    shiny::runApp(app)
}

app <- simpleafQCShiny(
    simpleafQuantDir = system.file("extdata/alevinfry_example_piscem_v0.6.0",
                                   package = "alevinQC"),
    sampleId = "example")
if (interactive()) {
    shiny::runApp(app)
}

csoneson/alevinQC documentation built on Nov. 6, 2024, 7:42 a.m.