LD decay plot from multiple .ld files (different linkage groups)

[avnitkr]

Hi,

I am trying to plot LD decay plot from five .ld files ( generated from five linkage groups). I used the following script to plot it-

module load R/4.0.0

Rscript --vanilla --slave /g/data/ht96/Avneet_UQ/ld_recombinant_pop/ld_decay/fit_LDdecay.R --ld_files /g/data/ht96/Avneet_UQ/ld_recombinant_pop/ld_decay/f11_ld_files.txt --fit_level 2 --out /g/data/ht96/Avneet_UQ/ld_recombinant_pop/ld_decay/f11_decay_plot.pdf

with my f11_ld_files.txt as
/g/data/ht96/Avneet_UQ/ld_recombinant_pop/ngsld/one/ngsld_lg_one.ld
/g/data/ht96/Avneet_UQ/ld_recombinant_pop/ngsld/two/ngsld_lg_two.ld
/g/data/ht96/Avneet_UQ/ld_recombinant_pop/ngsld/three/ngsld_lg_three.ld
/g/data/ht96/Avneet_UQ/ld_recombinant_pop/ngsld/four/ngsld_lg_four.ld
/g/data/ht96/Avneet_UQ/ld_recombinant_pop/ngsld/five/ngsld_lg_five.ld

I was able to generate a pdf plot but it looks uninformative or may be something is wrong with the list of my .ld files. I am trying to plot on ld decay plot from the five .ld plot. I would be grateful if you could help me with this issue. I am also attaching the output file that was generated from above script.
f11_decay_plot.pdf

[fgvieira]

Hi,

can you try playing a bit with the option --plot_size and --plot_scale?
Sometimes the script has a bit of trouble finding the best values...