zoom.plot: Zoom in manhattan plot with gene models and LD plotted below.
In sushilashenoy/zoom.plot: Modular zoom plots for genomic data

The zoom.plot function creates a png file with a zoom in manhattan plot and LD plot.

zoom.plot(pvals, gene.id, all.snps, snp.id = NULL, genotypes,
  window = 1e+06, min.snps = 10, color = "maf", ld.opts = NULL,
  ld.colors = NULL, img.height = 700, img.width = 1200, img.prefix = "",
  save.image = TRUE)

`pvals`	a vector where each pval corresponds to a single SNP, ordered by chromosome and position (same order as `all.snps`)
`gene.id`	either a gene or phenotype name. If this matches a cis gene, that gene will be drawn in a different color. The name is also used for the plot title.
`all.snps`	a data.frame containing one row for each snp (same order as pvals). The data.frame should have three named columns (in any order): id, chrom, and position. The snp order should match `pvals`.
`snp.id`	The snp that the plot will center on. If not specified we find the most significant one
`genotypes`	a matrix of genotypes with 0/1/2 coding for all snps, with snps in columns
`window`	window size, in bp, of chromosomal region to show in zoom plot. If there are more than a few hundred SNPs it can be very slow to calculate LD.
`min.snps`	This argument is included for compatibility with previous versions but DOES NOT DO ANYTHING.
`color`	This can be `'maf'` if the manhattan plot should be colored by minor allele frequency or `'het'` to color by percent heterozygotes. Any other value will give black points.
`ld.opts`	list of optional arguments for ld.matrix
`ld.colors`	color scale for LD plot (default white->red)
`img.height`	height of saved image
`img.width`	width of saved image
`img.prefix`	Any additional image prefix desired, in addition to the gene.id which is always included.
`save.image`	(default TRUE) set to false to plot with current device. Can be used to plot within R or to save with a different image format. This function was previously implemented in a standalone script (`'zoom_ld_biomart.r'`) which was largely based on code from G. Hoffman.) By default the most recent human gene ensembl database is used for gene models. To use a different database please use the `load.gene.mart()` function.