Plotting a heat map with Fst generated from dartR

[Zoriana Lam]

Hi,

I have calculated pairwise Fst using gl.fst.pop(). Not sure if this is a question relating to dartr or ggplot. Is there a way to plot a Fst heatmap using directly the Fst results output generated instead of creating the plot from the results using the 'hierfstat' package?

Cheers,

Zoriana

[Jose Luis Mijangos]

Hi Zoriana,

You can try:

> install.packages("dartR.base")
> library(dartR.base)
> res <- gl.report.fstat(possums.gl)

Cheers,

Luis 

[Zoriana Lam]

Hi Luis,

Thank you for the code! I have tried install the "dartR.base" package and tried to load the package but there is an error showing:

Registered S3 methods overwritten by 'dartR.base':
  method      from
  cbind.dartR dartR
  rbind.dartR dartR
Error: package or namespace load failed for ‘dartR.base’:
 .onAttach failed in attachNamespace() for 'dartR.base', details:
  call: gsub_(st$close, st$open, text, fixed = TRUE, useBytes = TRUE)
  error: could not find function "gsub_"

Not sure where the problem is.

Cheers,

Zoriana

[Bernd.Gruber]

Hi Zoriana,

 

Can you try to

 

to install rlang from CRAN

 

install.packages("rlang")

 

and see if that fixes ist.

 

Cheers, Bernd

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[Zoriana Lam]

Hi Bernd,

It seems that R doesn't allow me to download the package with the error:

Error in install.packages : Updating loaded packages

R has ask me to restart again in order to possibly download the package but it doesn't work. It happened with the same issue when I tried to download the "dartR.base" package as well.

Cheers,

Zoriana

[Bernd.Gruber]

Can you restart Rstudio and make and install from a R (before loading any package and be aware that you also do not start with a workspace loaded (as this might be already have some packages loaded). Make sure all Restores  are ticked off before you restart Rstiudio (and once installed tick the again so you have the restore option again).

 

 

 

So a fresh restarted R with no loaded packages and then try to install rlang.

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