alignK not working across values of K

[weeds23]

Hi,
I have created averaged barplots for each K using mergeQ, and would now like to plot them stacked together with each population cluster having the same colour across each plot. I had hoped to do this by first using alignK to align clusters across K as per the vignette (although in the vignette these were not averaged runs so I am not sure if this works) and then use plotQ. It plots the barplots for each K but the colours are not consistent across populations. AlignK seems to be aligning cluster assignments within each K, but not across all K. I have tried to do this both before and after averaging each K (see below) and neither works. I have confirmed that the object I'm using for alignK is in fact a qlist using is.qlist so I'm not sure why its not working.
Is there a way to achieve this for averaged plots? Sorry if this is simple, but I didn't see this specified in the vignette.
Here is example code, image attached of the plot I have so far:
#For K3. Repeated for each K
slist <- readQ(files=choose.files(multi=TRUE))
slist1 <- alignK(slist[c(1:10)]) #here alignK works
meanK3 <- mergeQ(slist1)

meanKs <- alignK(c(meanK3, meanK4, meanK5, meanK6, meanK7, meanK8)) #here it doesn't
is.qlist(meanKs)
poplabs <- read.table("Allpops_poplabels.txt", header=T)
plotQ(meanKs, imgoutput="join",
sortind=NA, grplab = poplabs, clustercol = clist$shiny,
returnplot=T, exportplot=F, basesize=11)

#I also tried aligning all runs of K before merging, but got the same end result:
slist3 <- readQ(files=choose.files(multi=TRUE))
slist4 <- readQ(files=choose.files(multi=TRUE))
slist5 <- readQ(files=choose.files(multi=TRUE))
slist6 <- readQ(files=choose.files(multi=TRUE))
slist7 <- readQ(files=choose.files(multi=TRUE))
slist8 <- readQ(files=choose.files(multi=TRUE))

Aligned <- alignK(c(slist3[c(1:10)], slist4[c(1:8)], slist5[c(1:10)], slist6[c(1:10)],
slist7[c(1:9)], slist8[c(1:9)])) #doesn't work
meanK3a <-mergeQ(Aligned[c(1:10)])
meanK4a <-mergeQ(Aligned[c(11:18)])
meanK5a <-mergeQ(Aligned[c(19:28)])
meanK6a <-mergeQ(Aligned[c(29:38)])
meanK7a <-mergeQ(Aligned[c(39:47)])
meanK8a <-mergeQ(Aligned[c(48:56)])
meanKs <- c(meanK3a, meanK4a, meanK5a, meanK6a, meanK7a, meanK8a)
p1 <- plotQ(meanKs,
sortind=NA, grplab = poplabs, clustercol = clist$shiny,
imgoutput="join",returnplot=T,exportplot=F,basesize=11)
grid.arrange(p1$plot[[1]]) #for some reason plotQ didn't work without using grid.arrange this time.

I have also tried importing all runs of all K together at the same time as one qlist, but this didn't make a difference.

Other issues: I am also having additional issues that may or may not be related. I thought the above problem could be because it was not recognising my tess2 files properly, so I re-imported them specifying the filetype within readQ and then received this error "Error in append(dlist, dfr) : object 'dfr' not found". So I then tried importing them with readQTess instead, and didn't get the error and they apparently imported OK. I am also not getting the grplabels appearing on the plot, but I didn't get an error about this.

[Nico-laF]

Hello!! :) Has this issue been sorted for you @weeds23 or did you find a workaround?
I am currently dealing with the same issues :/

[weeds23]

Hello!! :) Has this issue been sorted for you @weeds23 or did you find a workaround? I am currently dealing with the same issues :/

Hi @Nico-laF! No, unfortunately I didn't get any response and I couldn't get it to work after much trying of various different things, so I ended up using the CLUMPAK server (http://clumpak.tau.ac.il/) directly to align K and produce the figures instead and it worked! If you need any further help LMK.

[k0k0kk0]

CLUMPAK http://clumpak.tau.ac.il/ is notfound！help！ help！ help！

[k0k0kk0]

Hello!! :) Has this issue been sorted for you @weeds23 or did you find a workaround? I am currently dealing with the same issues :/

Hi @Nico-laF! No, unfortunately I didn't get any response and I couldn't get it to work after much trying of various different things, so I ended up using the CLUMPAK server (http://clumpak.tau.ac.il/) directly to align K and produce the figures instead and it worked! If you need any further help LMK.

CLUMPAK http://clumpak.tau.ac.il/ is notfound！help！ help！ help！