I am not sure whether this is an appropriate question for this board, but if anyone can help, I would be immensely grateful.
I am trying to create a figure for a publication, showing an overview of the bioinformatics steps taken in our study. The idea for this plot came from an answer that I saw here at BioStar: A: Best way to visualize Next Generation Sequencing tumor evolution in a graphic?. That plot was generated using ggplot2, I believe.
A bit of background about the information I want to have in this plot: at each step of the bioinformatics, we have a number of upregulated genes and downregulated genes. From one step to the next, the numbers usually become smaller, but not always. I want to show this with "step number" on the x-axis (step 1, step 2, etc.). I want to divide the y-axis into two: number of upregulated genes on the top half, and number of downregulated genes on the bottom. The way I envision this plot turning out, is that there are two lines (one for upregulated genes, one for downregulated genes) that smoothly meander from value to value as one moves from left to right on this plot, looking much like the one that I referred to earlier.
I am quite proficient in R, but have no experience with ggplot2 as yet, but I do have a copy of the ggplot2 book that I have just barely started reading through. So far I have not found out how to manage to execute this plan however. Can anyone advise me about how to get started with making this? Preferably not with MS Paint :-)