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SDP panel not working in plot_snpinfo() plots? #232

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kbroman opened this issue Mar 15, 2024 · 1 comment
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SDP panel not working in plot_snpinfo() plots? #232

kbroman opened this issue Mar 15, 2024 · 1 comment
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@kbroman
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kbroman commented Mar 15, 2024

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 kbroman added the bug label Mar 15, 2024
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kbroman commented Mar 15, 2024

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.

kbroman added a commit to kbroman/qtl2 that referenced this issue Mar 15, 2024
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Fix bug in plot_snpasso() re SDP panel (Issue rqtl#232)
b39f922
@kbroman kbroman closed this as completed Apr 5, 2024
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