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R: bisulfite squencing PCR plot

Hi All,

Do you have R code for the bisulfite sequencing PCR result plotting script.

Thanks

image: plot

bsp r
• 3,145 views • link
updated by Ram Ram • written by Shicheng Guo Shicheng Guo

3 answers

There might be a package that will produce those exactly, but if not you can do it in ggplot2:

d <- data.frame(CpG=rep(1:10,4), read=rep(1:4, each=10), value=sample(c(1,16), 40, replace=T))
ggplot() + scale_shape_identity() + geom_point(data=d, aes(x=CpG, y=read, shape=value), size=5)

Note that you'll need to tweak the size, remove the background, etc., but that should serve as a start.

• 0 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

I made a plotter that will start with PCR data and will also do nucleosome footprinting (NOMe-seq)

https://github.com/ying-w/bioinformatics-figures/tree/master/methylcircleplot

image:fig from paper

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updated by Ram Ram • written by Ying W Ying W

Thanks. Devon, It would be more perfect with the suitable setting: coord_cartesian

library("ggplot2")
d <- data.frame(CpG=rep(1:10,4), read=rep(1:4, each=10), value=sample(c(1,16), 40, replace=T))
ggplot() + scale_shape_identity() + geom_point(data=d, aes(x=CpG, y=read, shape=value), size=9)+coord_cartesian(ylim = c(0, 5))
• 0 views • link
updated by Ram Ram • written by Shicheng Guo Shicheng Guo

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