Sample names order in tables and plots

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1

Hi ,

Is there a way to specify the order in which the samples names will be displayed in MultiQC tables and plots (STAR - Alignment Scores, FastQC- Sequence Counts, etc)? It looks like they are sorted in alphabetical order now.

Thank you,
Cori A.

2

Hi @JHBI115,

There are a few different answers to this - the short one is “no” and the longer ones all start with “it depends”.

Could you elaborate on what you’re trying to do please?

Phil

3

Hi Phil,

Thank you for your reply.
We would like to be able to enforce the order in which the samples are displayed in graphs.
Professor Tang (CC-ed here) can specify which graph in particular would be more needed to have a custom order of the samples.

Thank you!
Corina

4

Ok thanks - more details of what kind of order you need would help.

Some typical things that some folks want to do is to group samples. An easy way to do that is to put the files into directories and use the --dirs flag to prefix the sample names. Then they will be grouped even when sorting alphabetically. See the docs for more info on this flag:

Another type of request along these lines is when sample names themselves are not particularly informative. If you have additional metadata outside of MultiQC then you can bulk rename samples during running as follows:

I hope this gets you started - feel free to provide more info for the kind of sorting you need and I can try to help further.

Phil

5

Hi,

We are just checking if there is any solution on the question below(documentation attached).
In summary, we need to be able to enforce the order in which the samples are displayed in graphs.

We are looking forward to your reply. Thank you !

Best,

Corina Antonescu
Bioinformatics Engineer
Johns Hopkins - Department of Genetic Medicine

(attachments)

Sample Order, 2024-05-07.pdf (170 KB)

6

Hi @JHBI115,

Can you elaborate on what your desired order is? Would any of my suggestions above help, for example using directory names to group things?

Phil

7

Hi Phil,

Thank you so much for the quick reply.

Yes, I ended up renaming the samples, although I was hoping that I dont have to clutter the plot with extra ids.

Thank you,
Corina

8

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