StuartJEBaird
commented
6 days ago Hi wym-m!
Natalia may be able to help you with the R implementation.
If not, get back to me - I can run your data through either the Mathematica or Python implementations.
(Breaking news: soon the circular 'iris plot' we have been publishing with will be available from R for data of any size).
Best
Stuart
On Wed, 20 Nov 2024 at 17:47, wmy-m @.***> wrote:
Hi Stuart and Natalia,
I am testing out diemR using whole genome data and I am having issues with plotPolarized.
My dataset seems to be too big and keep running into memory issues when plotting. `pdf("polarisedplot.pdf") plotPolarized(genotypes = genotypes, HI = h[1:222])
Error in dev.off() : 'R_Calloc' could not allocate memory (18446744073688835790 of 1 bytes) Execution halted ` This is using 160G of memory in SLURM. I have around 6 millions markers in the genotype file. Is there a way to plot subsets? Is there a way to retrieve scaffold/chr information and make plots by scaffolds/chr?
Thanks in advance!
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Hi Stuart and Natalia,
I am testing out diemR using whole genome data and I am having issues with plotPolarized.
My dataset seems to be too big and keep running into memory issues when plotting. `pdf("polarisedplot.pdf") plotPolarized(genotypes = genotypes, HI = h[1:222])
Error in dev.off() : 'R_Calloc' could not allocate memory (18446744073688835790 of 1 bytes) Execution halted ` This is using 160G of memory in SLURM. I have around 6 millions markers in the genotype file. Is there a way to plot subsets? Is there a way to retrieve scaffold/chr information and make plots by scaffolds/chr?
Thanks in advance!