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Can't read dotplot results #36

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Estherrr1997 opened this issue Mar 31, 2022 · 1 comment
Open

Can't read dotplot results #36

Estherrr1997 opened this issue Mar 31, 2022 · 1 comment

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@Estherrr1997
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Hi there,

I created a dotplot with pafR to compare large genomes,
altough I can't really read the dotplot since the lines of the figure (the raster) makes it hard
to see where the genomes are similair or not. I also tried to zoom in but that didnt work..
I will attach the output I get:

alignment_blue_shark_ss_cat_shark

Can you please help me with this? I could really use the results

Kind regards,
Esther

@Estherrr1997
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For anyone having this same issue:
Going into the pafR code and changing the linetype did it for me.

The code I changed:
if (dashes) {
p <- p + geom_hline(yintercept = c(seq_maps[["tmap"]], sum(unique(ali$tlen))), linetype = 0) +
geom_vline(xintercept = c(seq_maps[["qmap"]], sum(unique(ali$qlen))), linetype = 0)
}

By setting the linetype to 0 instead of 3, the dashes are invisible, generating a plot like this:
alignment_blue_shark_ss_cat_shark

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