Hello,
I'm trying to use the gl.map.snmf function and it does not appear in the viewer (just a blank gray area). There are some samples without lat/lon data, but the normal gl.map.interactive works fine with this data set.
I get the barplot with gl.plot.snmf, is there another way to reassign individuals to their snmf cluster? Similar to DAPC results with find.clusters I've used pop(gl) <- groups$grps (groups being the results of find.clusters)
Code being used:
four_5_7_accessions_snmf1 <- gl.run.snmf(four_5_7_accessions, minK=2, maxK=16, rep=10, verbose=1)
gl_Q <- gl.plot.snmf(snmf_result = four_5_7_accessions_snmf1, plot.K = 6, ind_name = T, border_ind = 0.15, plot.out = T, plot_theme= theme_bw(),color_clusters=paletteer_d("ggsci::nrc_npg", n=10))
four_5_7_accessions_map <- gl.map.snmf(four_5_7_accessions, qmat=gl_Q,
scalex = 1, scaley=1, movepops=NULL, pop.labels = T,
color_clusters=paletteer_d("ggsci::nrc_npg", n=10),
provider="Stadia.StamenTonerLite")
I get the bar plot with gl.plot.snmf, is there maybe another way to reassign individuals to their snmf cluster? Similar to DAPC results with find.clusters I've used pop(gl) <- groups$grps (groups being the results of find.clusters)
I see the gl_Q$Label and gl_Q$Cluster results but they are not tied together so the pop(gl) <- option didn't work.
Thank you,