plotGeneModel: Gene and mutation plotting

In jtlovell/hal2.fil2.compare: Compare HAL2 genome to FIL2 Reference

Description

plotGeneModel Given a gff file and snpeff annotated snp file, plot the mutations pertaining to a specific gene.

Usage

plotGeneModel(gff, snpEffVCF, geneID, upstreamBuffer = 1000,
  downstreamBuffer = 500, features2plot = c("exon", "five_prime_UTR",
  "three_prime_UTR"), colors = c("steelblue3", "lightsteelblue1",
  "lightsteelblue1"), mutations2annotate = c("missense", "stop", "start"),
  pchMutation = c(2, 8, 8), colMutation = c("darkblue", "darkred", "green"),
  orientation = NULL, windowSize = 100, stepSize = 10, scaleBar = 0.1,
  ...)

Arguments

gff	The gff file, must contain the following column names: chr, type, start, end, orientation, info
snpEffVCF	The snpeff annotated vcf file, must contain the following column names: CHR, POS, INFO, where info is the snpeff annotations
upstreamBuffer	How many bp upstream should be plotted
downstreamBuffer	How many bp downstream should be plotted
features2plot	What gff elements should be plotted?
colors	Colors for exon, 3'UTR and 5'UTR respectively
mutations2annotate	Partial string matching for types of differences to annotate
pchMutation	Shape of points that specify annotated sites
colMutation	Color of points that specify annotated sites
windowSize	Sliding window (for difference densities) window size
stepSize	Sliding window step size
scaleBar	If NULL, do not plot a scale bar, otherwise, specify the proportion of total gene space that the scale bar covers
...	additional arguments, not currently in use.

Value

a dataframe containing the annotated vcf file of Hal2 Fil2 differences for the gene specified in geneID

Examples

plotGeneModel(gff = gf, snpEffVCF = sev, geneID = "Pahal.C00786", windowSize=200, stepSize = 5)

jtlovell/hal2.fil2.compare documentation built on May 20, 2019, 3:14 a.m.