snplot: plot snp with gene
In guokai8/CandiHap: Build Haplotye and Generate Figures

Description Usage Arguments Value Author(s)

plot snp with gene

snplot(
  hap,
  gene,
  hapname = NULL,
  layout = "lolliplot",
  mutateOnly = FALSE,
  snp.colors = NULL,
  angle = 90,
  side = FALSE,
  type = "circle",
  rescale = FALSE,
  snp.alpha = 0.7,
  jitter = "node",
  random = TRUE,
  snp.lwd = 0.5,
  label.cex = 0.8,
  upstream = NULL,
  downstream = NULL
)

`hap`	SeqHap object include a GRanges, GRangesList
`gene`	character gene
`hapname`	haplotype want to display
`layout`	a character to indiate layout method (lolliplot or dandelion.plot)
`mutateOnly`	only show the alt is different with the REF or not
`snp.colors`	color for the snp, random colors will be used if NULL
`angle`	a numeric indicate the angle for the labels
`side`	use both top and bottom to display the SNP (TRUE/FALSE)
`type`	character. Could be circle, pie, pin, pie.stack or flag.
`rescale`	rescale the x-axis or not.
`snp.alpha`	alpha value for color
`jitter`	jitter the position of nodes or labels.
`random`	use random height to display SNP or not
`snp.lwd`	The line width for displaying SNP, a _positive_ number.
`label.cex`	label size
`upstream`	Defines the number of nucleotides toward the 5'
`downstream`	Defines the number of nucleotides toward the 3'