Fine-mapping results not showing

statgen / locuszoom-standalone

Create regional association plots from GWAS or meta-analysis

http://locuszoom.org/

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Fine-mapping results not showing #10

Closed Zepeng-Mu closed 4 years ago

Zepeng-Mu commented 4 years ago

Hi,

I am trying to plot my own fine-mapping results to the LocusZoom plot. However, sometimes the fine-mapped region is omitted in the plot, and sometimes it shows fine.

For example, in one region, I could see the coordination is 1.5-1.58 Mb on Chr9. In the output table of fine-mapping regions, there are two SNPs that fall in this region. But these two SNPs (in the same credible set) are not shown in the plot. I also include the example here.

Thank you so much!

welchr commented 4 years ago

My guess is that it's dropping all of those extra groups because the default number of finemapping rows is 3 (hence the "6 regions omitted.")

Could you try setting the number of rows to some large number, like:

locuszoom <your options here> fmrows=99

Does that work?

Zepeng-Mu commented 4 years ago

I think it is working now. Thank you so much! But when I set fmrows=99, the fine-mapping track becomes so wide that the GWAS catalog tracking I am using got pushed out of the page, so I guess I still need to play with the parameter a bit.

welchr commented 4 years ago

Good to hear. Some other settings that might help:

height: set the height of the PDF in inches (default is 7). That would give you a little more space.
gwrows: set the maximum number of rows for GWAS catalog (default is 3)
rfrows: set the maximum number of rows for genes (default is 10)