Alternative links - placement of mutation ticks

[naurasd]

Hi,

I noticed that the mutation ticks are placed in two different ways on the links between haplotypes, depending on if it's an alternative or regular link.

In the network below, check the alternative link between ASV39 (the largest one) and ASV1358. You can see that the mutation ticks are placed on the center of a line between the CENTERS of both haplotypes so the ticks have and equal distance to the CENTERS of each haplotype. However, mutation ticks of regular links seem to be placed on the center of a line between the EDGE of haplotypes so the ticks have and equal distance to the EDGE of each haplotype.

Unfortunately, in this way, the mutation ticks of alternative links seem a bit out of place. Is there a way to have them drawn with an equal distance from the edges of two haplotypes instead of from the centers of two haplotypes?

Cheers

Nauras

[emmanuelparadis]

This is fixed. I've pushed a new version here (1.2-0.2). You'll need to re-install from GitHub because the changes are in internal functions. Cheers,

[naurasd]

Thanks, much appreciated.

I tried

devtools::install_github("emmanuelparadis/pegas")

but this gave an error

Downloading GitHub repo emmanuelparadis/pegas@HEAD
Error: Failed to install 'pegas' from GitHub:
  Does not appear to be an R package (no DESCRIPTION)

What do I need to do in order to install from Github?

[emmanuelparadis]

You need to double 'pegas':

devtools::install_github("emmanuelparadis/pegas/pegas")

[naurasd]

Worked, thanks ;-)

[naurasd]

Hi,

i just realized that with the new version, this works for mutation ticks. But with show.mutaion = 2 for example, this is still not working.

Cheers Nauras

[emmanuelparadis]

Hi, This should be fixed. I've pushed here (same version number but new date). Cheers, Emmanuel

[naurasd]

Works perfectly ;-) Thanks