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rqtl / qtl2

QTL analysis software for high-dimensional data and complex cross designs
https://kbroman.org/qtl2
GNU General Public License v3.0
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SDP panel not working in plot_snpinfo() plots? #232

Closed kbroman closed 6 months ago

kbroman commented 6 months ago

The strain distribution pattern (SDP) panel in the plot of SNP association results doesn't seem to be working. See the 2nd-to-last figure in the user guide. There are supposed to be vertical lines at each SNP, but they're not showing. (Maybe they're just too thin to be viewed?)

The plot_sdp() example does seem to work.

kbroman commented 6 months ago

Seems to be an issue of snpinfo$snp vs snpinfo$snp_id. The latter is used to select the SNPs showing in the SDP panel, but former is used in other cases.