Changing mutation rate

[cmtom]

Hello,

I'm curious why the ***.ltr.insert.density.pdf plot densities change in an order of magnitude if you change the mutation rate, but the ***.ltr.insert.histo.pdf remains the same. I anticipated that only the x-axis would change with the new mutation rate, but somehow the density (y-axis) of LTRs change as well. I attached the small genome example ran as default and with a different mutation rate of -mu 6.7e-09.

I used the default example script then I ran this:

prefix=Arabidopsis_suecica
DT=date +"%y%m%d%H%M"
options="-pre ${prefix}_" # to avoid conflicts
subphaser -i ${prefix}_genome.fasta.gz -c ${prefix}_sg.config -max_memory 128G -disable_circos -intact_ltr -mu 1.75e-09 $options 2>&1 | tee ${prefix}.log.$DT

I checked without the -intact_ltr flag and the results are the same.

Any insights would be greatly appreciated.

Arabidopsis_suecica_k15_q200_f2.ltr.insert.histo.default.pdf
Arabidopsis_suecica_k15_q200_f2.ltr.insert.density.1.75.pdf
Arabidopsis_suecica_k15_q200_f2.ltr.insert.histo.1.75.pdf
Arabidopsis_suecica_k15_q200_f2.ltr.insert.density.default.pdf

Thank you.
Crystal

[zhangrengang]

I think the y-axis (density) may depend on the x-axis: when Δx is higher, y is lower, vice versa.
It is coded with ggplot2 which can be found in *.ltr.insert.R:

geom_line(stat="density", size=1.5)

You may discuss with the authors of ggplot2 or learn sonething about the algorithm of kernel density, as I am not clear about the deep details of density plot.