A small suggestion for a minor improvement I see in the all nf-core #taxprofiler

A small suggestion for a minor improvement: I see ...

Håkon Kaspersen

10/08/2025, 1:58 PM

A small suggestion for a minor improvement: I see in the "all samples" plots from nonpareil that the legend is mushed up over the plot area. Is this something that nonpareil does when plotting, or can the legend be moved to the outside of the plot? See attached figure f. ex.

James Fellows Yates

10/09/2025, 3:23 AM

These are the options for the script that makes that pllot:

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$ NonpareilCurves.R --help
Usage: /home/james/bin/miniforge3/envs/nonpareil/bin/NonpareilCurves.R [options] sample1.npo [sample2.npo ...]                                                  
                                                                                
                                                                                
Options:                                                                        
	--labels=SAMPLE1,SAMPLE2,...
		Labels to be used for the samples

	--json=FILE
		Output file, Nonpareil curve processed data in JSON format

	--tsv=FILE
		Output file, Nonpareil curve summaries in TSV format

	--csv=FILE
		Output file, Nonpareil curve summaries in CSV format

	--pdf=FILE
		Output file, Nonpareil curve plot in PDF format

	--pdf-size=WIDTH,HEIGHT
		Width and height of the PDF file (if --pdf)

	--xlim=FROM,TO
		Minimum and maximum points in the X-axis (in bp, if --pdf)

	--col=COL1,COL2,...
		Colors to be used for the Nonpareil curves (if --pdf)

	--no-observed
		Do not plot observed curves (if --pdf)

	--no-model
		Do not plot model curves (if --pdf)

	-h, --help
		Show this help message and exit

James Fellows Yates

10/09/2025, 3:23 AM

So maybe you could try doing something like this in a config file:

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profile {
    withName: NONPAREIL_NONPAREILCURVESR {
        ext.prefix = { "nonpareil_all_samples" }
        ext.args = "--pdf-size 200,200 --xlim=200"
        publishDir = [
            path: { "${params.outdir}/nonpareil/" },
            mode: params.publish_dir_mode,
            pattern: '*.{json,csv,tsv,pdf}',
        ]
    }
}

Or something and see what happens? Unfortunately it's not something the tool supprots dynamically... I guess we could make pipeline level parameters. But to get the right size for you now, you could go into th

work

directory of

NONPAREIL_NONPAREILCURVESR

, iteratively modify

.command.sh

to add the

--pdf-size

stuff, and run

bash .command.sh

until you get the right size?

🙌 1

Håkon Kaspersen

10/09/2025, 10:55 AM

Thanks for suggestions! Totally understand that it's not easy to adjust figures for different sample sizes, but this tip will likely work fine. Thanks!

👍 1

James Fellows Yates

10/09/2025, 10:56 AM

(or just re-run manaklly)

🙌 1

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