Generate a report summarizing the main aspects of an alevin/alevin-fry quantification run. The report generation assumes that alevin/alevin-fry has been run with the –dumpFeatures flag to generate the necessary output files.
alevinQCReport(
baseDir,
sampleId,
outputFile,
outputDir = "./",
outputFormat = NULL,
showCode = FALSE,
forceOverwrite = FALSE,
knitrProgress = FALSE,
quiet = FALSE,
ignorePandoc = FALSE,
customCBList = list(),
...
)
simpleafQCReport(
simpleafQuantDir,
sampleId,
outputFile,
outputDir = "./",
outputFormat = NULL,
showCode = FALSE,
forceOverwrite = FALSE,
knitrProgress = FALSE,
quiet = FALSE,
ignorePandoc = FALSE,
customCBList = list(),
...
)
alevinFryQCReport(
mapDir,
permitDir,
quantDir,
sampleId,
outputFile,
outputDir = "./",
outputFormat = NULL,
showCode = FALSE,
forceOverwrite = FALSE,
knitrProgress = FALSE,
quiet = FALSE,
ignorePandoc = FALSE,
customCBList = list(),
...
)(Only used for alevin output) Path to the output directory
from the alevin run (should be the directory containing the
alevin directory).
Sample ID, will be used to set the title for the report.
File name of the output report. The file name extension
must be either .html or .pdf, and consistent with the value
of outputFormat.
Path to the output directory where the report will be generated.
The format of the output report. Either
"html_document", "pdf_document",
"BiocStyle::html_document" or "BiocStyle::pdf_document".
The file name extension of outputFile must be consistent with this
choice.
Logical, whether to display the R code in the report.
Logical, whether to force overwrite an existing report with the same name in the output directory.
Logical, whether to display the progress of knitr
when generating the report.
Logical, whether to show progress messages.
Logical, determines what to do if pandoc or
pandoc-citeproc is missing (if Sys.which("pandoc") or
Sys.which("pandoc-citeproc") returns ""). If ignorePandoc
is TRUE, only a warning is given. The figures will be generated, but not
the final report. If ignorePandoc is FALSE (default), the
execution stops immediately.
Named list with custom set(s) of barcodes to provide summary statistics/plots for, in addition to the whitelists generated by alevin.
Other arguments that will be passed to rmarkdown::render.
(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).
(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).
(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).
(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).
Generates a summary report in the outputDir directory, and
returns (invisibly) the name of the generated report.
When the function is called, a .Rmd template file will be copied
into the output directory, and rmarkdown::render will be called to
generate the final report. If there is already a .Rmd file with the same
name in the output directory, the function will raise an error and stop,
to avoid overwriting the existing file. The reason for this behaviour is
that the copied template in the output directory will be deleted once
the report is generated.
alevinQCReport(
baseDir = system.file("extdata/alevin_example_v0.14",
package = "alevinQC"),
sampleId = "example", outputFile = "alevinReport.html",
outputDir = tempdir(), forceOverwrite = TRUE)
#> Warning: unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
#> dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 0x0006): Library not loaded: /opt/X11/lib/libSM.6.dylib
#> Referenced from: <9787D5C5-915A-33A4-A4E0-4C500143DC8D> /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/modules/R_X11.so
#> Reason: tried: '/opt/X11/lib/libSM.6.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libSM.6.dylib' (no such file), '/opt/X11/lib/libSM.6.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libSM.6.dylib' (no such file), '/Users/runner/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.5-11.0/arm64/Contents/Home//lib/server/libSM.6.dylib' (no such file)
#> Warning: unable to load shared object '/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so':
#> dlopen(/Library/Frameworks/R.framework/Resources/library/grDevices/libs//cairo.so, 0x0006): Library not loaded: /opt/X11/lib/libXrender.1.dylib
#> Referenced from: <C6A11057-3B07-39E4-BC6D-BF4311277098> /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/grDevices/libs/cairo.so
#> Reason: tried: '/opt/X11/lib/libXrender.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libXrender.1.dylib' (no such file), '/opt/X11/lib/libXrender.1.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libXrender.1.dylib' (no such file), '/Users/runner/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.5-11.0/arm64/Contents/Home//lib/server/libXrender.1.dylib' (no such file)
#> Warning: failed to load cairo DLL
#> Warning: failed to load cairo DLL
#> Error in dev.control(displaylist = if (record) "enable" else "inhibit"): dev.control() called without an open graphics device
#>
#> Quitting from lines 30-40 [prep] (alevinReport.Rmd)
alevinFryQCReport(
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", outputFile = "alevinFryReport.html",
outputDir = tempdir(), forceOverwrite = TRUE)
#> Warning: failed to load cairo DLL
#> Warning: failed to load cairo DLL
#> Error in dev.control(displaylist = if (record) "enable" else "inhibit"): dev.control() called without an open graphics device
#>
#> Quitting from lines 43-47 [setup-alevin] (alevinFryReport.Rmd)
simpleafQCReport(
simpleafQuantDir = system.file("extdata/alevinfry_example_piscem_v0.6.0",
package = "alevinQC"),
sampleId = "example", outputFile = "simpleafReport.html",
outputDir = tempdir(), forceOverwrite = TRUE)
#> Warning: failed to load cairo DLL
#> Warning: failed to load cairo DLL
#> Error in dev.control(displaylist = if (record) "enable" else "inhibit"): dev.control() called without an open graphics device
#>
#> Quitting from lines 43-47 [setup-alevin] (simpleafReport.Rmd)