problem plotting scan1snps results when keep_all_snps=FALSE

[kbroman]

Was working with the Arabidopsis MAGIC data and trying to create SNP info from available founder snps, and ran into an error when plotting the results of scan1snps().
Basic set up of data:

file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/master/ArabMAGIC/arabmagic_tair8.zip")
arab <- read_cross2(file)

gmap <- insert_pseudomarkers(arab$gmap, step=1)
pmap <- interp_map(gmap, arab$gmap, arab$pmap)

pr <- calc_genoprob(arab, gmap, error_prob=0.002, cores=0)

Prepare snp info:

library(qtl2convert)

snpinfo <- map_list_to_df(arab$pmap, marker="snp")
fg <- do.call("cbind", arab$founder_geno)
sdp <- calc_sdp(t(fg))

snpinfo <- cbind(snpinfo[names(sdp),], sdp)
snpinfo <- index_snps(pmap, snpinfo)

This works:

out_snps <- scan1snps(pr, pmap, arab$pheno, snpinfo=snpinfo, keep_all_snps=TRUE)
plot(out_snps$lod, out_snps$snpinfo)

But this gives an error:

out_snps <- scan1snps(pr, pmap, arab$pheno, snpinfo=snpinfo)
plot(out_snps$lod, out_snps$snpinfo)

But it seems that this works fine:

out_snps <- scan1snps(pr, pmap, arab$pheno, snpinfo=snpinfo)
plot(out_snps$lod, snpinfo)