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niuhuifei / popoolation2

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Strange Patterns when graphing outputs #21

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Hello I am writing because I get a strange pattern when I visualize data output 
from Popoolation2 in R.  

I am comparing two populations.  I use the allelefreq_pwc and allelefreq_rc 
output files from the command perl <popoolation2-path>/snp-frequency-diff.pl to 
graph the major allele frequency in the first population against the allele 
frequency difference between the two populations..I would expect for this graph 
to look quite random however I see quite a few, and distinctive, vertical and 
horizontal lines.  This data set is not the only one where we have seen 
patterns of this nature.  What causes these patterns in the data.  I have 
attached the image of the graph

Best, 
Alyssa

Original issue reported on code.google.com by alyssa.w...@gmail.com on 10 Dec 2014 at 1:48

GoogleCodeExporter commented 9 years ago 
hi alissa,
can you please send me this graph as an email?
rokofler at gmail dot com
cheers ro

Original comment by RoKof...@gmail.com on 24 Jan 2015 at 10:51