How To Plot This Kind Of Ma-Plot?

Question

[Zhu]

Hi, there. i need helps on plot such kind of graph now.

the graph i linked here is from a paper about DEGs based on RNA seq.

i have tried the DEGseq package but the output graph is not like the one i linked and i have heard that the plotSmear function of edgeR package is capable of plot this kind of graph but i am not able to understand because the output graph looks similar to the DEGseq one.

any packages may do this work?

[Sean Davis]

You can do this in R relatively easily. What have you tried? From where are the data coming?

[Michael]

the 'alt text' tells me that you tried to paste in the image, but that didn't work. You need to host your image somewhere and provide the link, Biostar doesn't host images.

[Neilfws]

Please improve this question (link to image, better tags, explain what you have tried) or it will be closed.

[Michael]

Sorry but we don't see anything...

Answer 1

[seidel]

You don't need a package to construct an MA plot. Any plotting software will do. You simply have to create your x (the A part of the MA plot) and y (the M part) components appropriately. The purpose of the MA plot is to view a ratio of two things, as a function of the magnitude of those same two things. Thus if you have two things you'd like to compare, i.e. wt and mut, you create a ratio:

y = log2(mut/wt)

and for the x-axis you combine wt and mut to get a magnitude (geometric mean):

x = log2(sqrt(wt*mut))

Then you simply plot x against y. You could do it in excel, or R, or whatever - the package doesn't matter. The components of what you are plotting matter. MA plots simply make a nice way to view large numbers of ratios.