## this function integrates 3 steps to creating a genome plot
## 1 query bioMart to get a GFF like data-frame from ensembl
## 2 add new elements to the gff to make it plot with ggplot2
## 3 plot it with ggplot2
## the reason to split it like this is so that basic users may use this simple function
## and advanced users can try custom queries or altered plotting themes with the sep functions
 
gnmplot= function(filters='hgnc', values='MAF', species='human')
{
require(biomaRt); require(ggplot2)
 
gff= getGFF(filters=filters, values=values, species=species)
 
gff_new=alterGFF()
 
gnmplot=gffplot(gffnew)
 
return(gnmplot)
 
}