AlignK not working with increasing numbers of samples

[mcfiston]

alignK_not_working.zip

The alignK step seems to work fine for me in some situations but not others. Example below run in exactly the same way is using the same dataset twice but with more individuals in the 2nd case. For example: In the first case ("working") you can see that in the plot, the right hand three individuals are correctly changed to dark blue, whereas in the second case ("not working") that same cluster on the right hand side (now 7 individuals) are not changed. Any idea why this would be?

Super nice program - thank you!!

`

alignK seems to work fine here

sfiles <- list.files(path="/path/working/", full.names=T)
slist <- readQ(sfiles)

p1 <- plotQ(slist,imgoutput="join",returnplot=T,exportplot=F,basesize=11)
grid.arrange(p1$plot[[1]])

slist1 <- alignK(slist)
p2 <- plotQ(slist1,imgoutput="join",returnplot=T,exportplot=F,basesize=11)
grid.arrange(p1$plot[[1]], p2$plot[[1]], ncol = 2)

But once I add more individuals it stops aligning them

sfiles <- list.files(path="/path/notworking/", full.names=T)
slist <- readQ(sfiles)

p1 <- plotQ(slist,imgoutput="join",returnplot=T,exportplot=F,basesize=11)
grid.arrange(p1$plot[[1]])

slist1 <- alignK(slist)
p2 <- plotQ(slist1,imgoutput="join",returnplot=T,exportplot=F,basesize=11)
grid.arrange(p1$plot[[1]], p2$plot[[1]], ncol = 2)`

[sekhwal]

Did you try online version? http://pophelper.com/

[mcfiston]

Yes - I have tried there but even with the "working" dataset above I get an error message that says "Cannot Align/Merge runs. Value of K differs between selected runs." I am confused by that because I thought that alignK was supposed to align between K's? Attached is an image of before aligning (on online version) and error message when trying to align. I also attach a figure showing what I think it should look like where I have manually aligned the colours in excel

manually_aligned.pdf
online_alignK.pdf
online_unaligned.pdf

[eugeniadat]

Hi,
I am having the same issue, both with R and pophelperShiny.
Are there any updates about this issue?
I really want to use this powerful tool for my analyses but this issue makes my plots really hard ro read.
Thanks!

[cjfiscus]

Just ran into this issue myself using R package 2.3.1 trying to align K across K = 2-4 for 1225 individuals. Is there a solution in the works?

[cjfiscus]

To clarify, I attempted to first align K between 10 runs of the same K (this works as intended), but then attempted to align between K (this doesn't work). Code snippets are as follows:

`
k2<-mergeQ(alignK(slist[c(21:30)]))

k3<-mergeQ(alignK(slist[c(31:40)]))

k4<-mergeQ(alignK(slist[c(41:50)]))

out<-alignK(c(k2,k3,k4))
`
When plotted manually, the result is this, which is obviously not aligned between K:

This is the result of manual alignment and should be the result:

[juliannasantoseco]

I aligned K across the entire slist and it worked.

slist <- alignK(slist, type = "across")

p <- plotQ (slist[c(20, 40)],
imgoutput = "join", returnplot=T, exportplot=F, showdiv=T,basesize=11,
showyaxis = T, showticks=T, panelspacer=0.4, ticksize=0.3, ticklength=0.1,
sortind = "all", barsize = 1, barbordercolour = "darkgrey",
useindlab = T, showindlab = T, sharedindlab=F,
sppos = "right",
showlegend = T, legendkeysize = 10, legendtextsize = 10,
splab = spnames[c(20, 40)], # apply strip panel names
splabcol = "black", splabface = "italic", splabsize = 10, # strip panel label appearance
clustercol = brewer.pal (n = 4, name = "Dark2"))