I have been looking at a number of the tools available to create gene maps, things like ggbio, gviz, genoplotR, geneplotter, but I have not been able to find an example of what I am trying to do, so any suggestions would be much appreciated. I'm a relative new-comer to R/programming in general so please be as explicit/detailed as possible.
I have identified in my RNAseq that there is a 120kb region of my bacterial megaplasmid that is heavily affected by my experimental conditions. I'd like to make a map of that region, showing all of the genes, and have each genes coloured "fill" be the log2 fold change from my data.
I've also identified a motif that is significant, that I'd like to highlight on this map as well. I'd need to create the annotation for that myself, I currently have the coordinates of the motif within the 200 bp upstream of each of the affected genes.
As I've been looking at the various tools, one thing that does not seem to be explicity mentioned that is confusing me, is what type of data/input the programs take. I have the genomic data in EMBL and genbank format - is that suitable, or do I need some other type of input file?
