snptrack: plot Gene Track with SNP information
In guokai8/CandiHap: Build Haplotye and Generate Figures

plot Gene Track with SNP information

snptrack(
  obj,
  dat,
  id = "gene_id",
  color = NULL,
  chr = NULL,
  region = NULL,
  allchr = FALSE,
  gene = NULL,
  threshold = -log10(1e-06),
  geneOnly = FALSE,
  exonOnly = FALSE,
  upstream = 1000,
  downstream = 1000,
  alpha.point = 0.75,
  point.size = 1,
  point.shape = 20,
  exon = "darkgreen",
  utr3 = "cyan4",
  utr5 = "cyan4",
  intron = "black",
  gene.label.size = 0.5,
  high = "cyan4",
  low = "lightblue",
  threshold.col = "red",
  threshold.lwd = 1,
  threshold.lty = 2,
  ylab = "-log10 (P value)",
  legend.lab = NULL,
  ylab.size = 0.9,
  arrow.col = "lightblue",
  arrow.fill = "lightblue"
)

`obj`	Granges object include gff file
`dat`	Granges object include GWAS results
`color`	color for the point
`chr`	chromosome name
`region`	a vector include the start and the end location
`allchr`	choose TRUE when displaying whole chromosome or large region
`gene`	gene name
`threshold`	threshold to add the line
`geneOnly`	only show points in the gene region
`exonOnly`	only show points in the exon region
`upstream`	upstream bp
`downstream`	downstream bp
`alpha.point`	alpha
`point.size`	size of the point
`point.shape`	shape of the point
`exon`	exon color
`utr3`	3'utr color
`utr5`	5'utr color
`intron`	intron color
`gene.label.size`	size of the gene label
`high`	legend color
`low`	low legend color
`threshold.col`	color for threshold line
`threshold.lwd`	line width for threshold line
`threshold.lty`	line type for threshold line
`ylab`	ylab name
`ylab.size`	ylab size
`arrow.col`	arrow color
`arrow.fill`	arrow fill