Options for gl.plot.structure()

[Peter K]

Hi folks, a couple of hopefully a fairly quick queries:

How can I change the x-axis font size and plot margins for my Structure plots using gl.plot.structure()? (need to allow more space so that longer id names display fully)

Also how to change (or retain) the sort order (i.e. what are valid options for sort =  ), while subsetting my data set (so I the can display the genotypes for my full data set across a few different subplots so that the individual labels are not too crowded)?

Otherwise, how to set the x-axis labels to simply display the populations rather than the individual genotypes?

Thanks, Peter

[Jose Luis Mijangos]

Hi Peter,

We're still working on the customisation of the Structure plot.

In the meantime, you could use the code below.

Cheers,

Luis

devtools::install_github("EricArcher/strataG")

library(strataG)
library(dartR)
bc <- bandicoot.gl[,1:100]
sr <- gl.run.structure(bc, k.range = 2:5, num.k.rep = 3, exec = './structure.exe')
ev <- gl.evanno(sr)
qmat <- gl.plot.structure(sr, k=3, CLUMPP="./")

qmat_plot_tmp <- qmat
# preparing data
qmat_plot_tmp$ID <- paste0(qmat_plot_tmp$orig.pop,"_",qmat_plot_tmp$id)
qmat_plot_tmp <- qmat_plot_tmp[,-c(1:3)]
qmat_plot <- reshape2::melt(qmat_plot_tmp,id="ID")
#ordering data
qmat_plot <- qmat_plot[order(qmat_plot$ID),]
#plot
ggplot(qmat_plot, aes(x=ID, y=value, fill=variable))+
  geom_col(color="black") +
  theme_classic() +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) +
  ylab("Ancestry proportion") +
 xlab("") +
  labs(fill = "K")
 

[Peter K]

Great. Thanks Luis. That code seems to work fine and I should be able to adjust ggplot() options as required for other data sets.

Cheers,

Peter

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