Plotting genotype frequency distribution
Hi All,
I am planning to detect possible strand issues by checking genotype frequencies against population allele frequencies. for this, I am using Plugin af-dist from BCFtools.
I am following all the steps as mentioned in manual HERE. But, I am not able to plot The genotype frequency distribution, in this case, the data is
PROB_DIST 0.000000 0.100000 100618
PROB_DIST 0.100000 0.200000 144103
PROB_DIST 0.200000 0.300000 214923
PROB_DIST 0.300000 0.400000 320721
PROB_DIST 0.400000 0.500000 817965
PROB_DIST 0.500000 0.600000 84027
PROB_DIST 0.600000 0.700000 86531
PROB_DIST 0.700000 0.800000 97986
PROB_DIST 0.800000 0.900000 108776
PROB_DIST 0.900000 1.000000 176755
please help me in plotting this, I am looking to plot something like This
Thanks a lot for your help
Have a great day,
Dave!
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Kevin Blighe
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David_emir
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David_emir
1 answer
Dave, this should give you a good start:
plot(test[,2], type="l", xlab="Genotype Probability (HWE)", ylab="Frequency", lwd=3, col="orange")
lines(test[,3], type="l", lwd=2.5, col="skyblue")
legend("bottomright", bty="n", c("incorrect strand","correct strand"), fill=c("orange","skyblue"))
If you want to add extra axes a ticks, then just use something like:
axis(side=4, labels=FALSE)
You can take a look at these functions to see all other available options.
Kevin
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