qQCReport Missing Plots Described in Documentation
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Dario Strbenac ♦ 1.5k
@dario-strbenac-5916
Last seen 2 days ago
Australia

According to the documentation, there are eight kinds of plots generated by qQCReport. However, I only see four.

library(QuasR)
testFile <- system.file("extdata", "ex1.bam", package="Rsamtools")
qQCReport(testFile, "testQC.pdf")

Can the function's result be changed to match the documentation? Also, each plot is very small and takes up a small part of a large A4 PDF page, which affects plot legibility. QuasR version 1.22.1 is used.

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@hotz-hans-rudolf-3951
Last seen 4 months ago
Switzerland

Hi Dario

The number of plots you get depends on the input, e.g. if you run qQCReport on a qproject generated from paired-end fastq files, you will get 8 plots.

The plot sizes have been optimised to display several samples per page.

Hope this helps/clarifies Regards, Hans-Rudolf

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But the documentation ?qQCReport provides a list of seven plots which may be generated for any BAM file and an eighth plot which is for BAM files containing paired reads. The test file I used has paired reads

samtools view -c -f 1 Rsamtools/extdata/ex1.bam
3307

So, I expect to get eight plots but I only get four. Could you run the test code to check how many plots you obtain? The documentation of qQCReport and its output seems inconsistent.

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Yes, I agree the documentation is misleading (or even partly wrong). I will talk to the QuasR developers and try to get the documentation improved for of qQCReport.

Hans-Rudolf

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Hi Dario

The documentation and also plotting issues have been addressed in QuasR 1.23.17 (will become available in BioC-devel in a day or so).

The documentation has been simplified to make it clear that some plots will not be available if the necessary information is missing (e.g. base quality plots when working with a fasta file). Furthermore, qQCReport now has a new argument a4paper (a4paper = TRUE by default) that allows you to switch off the page-optimised layout for mapping and uniqueness plots.

Thank you for your report.

Michael

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