Warning in EnhancedVolcano plot
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Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 26 days ago
Munich, Germany

When running a volcano plot I get the following warning

1: ggrepel: 18 unlabeled data points (too many overlaps). Consider increasing max.overlaps

Where can i set the max.overlap parameter in the function?

thanks

Assa

volcano-plot EnhancedVolcano • 474 views
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@kevin
Last seen 1 hour ago
Naas, Republic of Ireland

Hi Assa,

I recently updated EnhancedVolcano to adjust for recent underlying changes in ggrepel.

You should download the GitHub version of EnhancedVolcano (https://github.com/kevinblighe/EnhancedVolcano), for now, and set a value for maxoverlapsConnectors, which is the equivalent of max.overlap:

remotes::install_github('kevinblighe/EnhancedVolcano')

General aesthetics have improved in this latest version, which will be released with the next Bioconductor official release, and I will recommend to always enable drawConnectors in the future.

Kevin

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Thanks for this. I had the same issue as the above user and this install fixed it. However, it created a new issue where connectors are not rendered for every labeled point (only ~50% of data points show a connector), whereas in the old version it works perfectly.

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Hey Charles, yes, thank you for bringing this up. You can set the following parameter so that it will draw connectors to everything:

maxoverlapsConnectors = Inf

...or, perhaps you tried this? At some point, I think, it will simply not have space to render everything.

Are you noticing the function giving any other messages about unused parameters?

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Hi Kevin, thanks for your reply.

Just to clarify, the "unlabeled data points" error message is presented in the old version which lacks the maxoverlapsConnectors argument.

When I use the newer version from your github link in order to make use of this argument (which I set it to 100, despite only having 18 labels to show), it gives no error message and shows all labels, but only renders a few of the actual connectors (i.e. many points have a label on the plot, but show no visible connector).

In the old version, every label that is rendered has its corresponding connector, but it I lose a few labels as a consequence of not having the "maxoverlapsConnectors" argument.

No other error messages from either old or new versions

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Hi, I see what you mean - thanks for clarifying. I have no explicit parameter that results in the rendering of all connectors. The function uses a mixture of connectors and no connectors to fit as many labels as possible. If you want connectors for everything, you could try to modify lengthConnectors and/or directionConnectors

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Ok I understand. I'll play around with these. Thank you!

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Sorry, one more quick reply. So, changing lengthConnectors and/or directionConnectors doesn't let me render any more connectors, but I found a quick fix for the old version.

If you load ggrepel separately and re-set its default options for your R session using something like options(ggrepel.max.overlaps=Inf), this change gets applied when EnhancedVolcano calls ggrepel, letting your render more labels.

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Thanks - that is interesting to know.

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