gl.plot.structure

[Juliana Souza]

Hi dartR team, 

I have some simples questions related to plotting the results for the structure run. 

1. When using clumplak = T (k=2), we get the plots for 2.1 and 2.2. I was wondering if it would be possible to get only one plot (i.e. only 2.1). Something similar to the clumpak simulation online. 

2. We need to change the font size for the individuals names. Are there any built in options? 

Best regards,

Juliana

[Jose Luis Mijangos]

Hi Juliana,

I added the option to plot just one plot (k_name), see text in bold red in the code below. 

You need first to install the developing version of dartR.popgen as shown below.

You can also see in the code below how you can modify the font of the individual labels using the parameter "size" also in bold red.

Cheers,

Luis 

library(devtools)
#install developing version of dartR.popgen
install_github("green-striped-gecko/dartR.popgen@dev")
library(dartR.popgen)
t1 <- platypus.gl
t1 <- gl.filter.callrate(t1,threshold = 1)
t1 <- gl.filter.monomorphs(t1)
res_struc <- gl.run.structure(t1,
                              exec = "./structure",
                              k.range = 2:4,
                              num.k.rep = 3,
                              burnin = 1000,
                              numreps = 1000,
)

# plotting results
r1 <- gl.plot.structure(res_struc,
                        k_name = "3.1",
                        plot.out = TRUE,
                        plot.file = "test",
                        plot.dir = getwd())
# reading rds file with plot
p1 <- readRDS("test.RDS")
# change the font size for the individuals name
p1 +
  theme(
    axis.text.x = element_text(
      size = 14,
      angle = 90,
      vjust = 0.5,
      hjust = 1
    )
  )

[Juliana Lopes]

Dear Dr. Mijangos,

The adjustments worked perfectly. 

Thank you very much,

Juliana

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