plotGeneModel: A plotting method for gene models

In jtlovell/qtlTools: Data Processing and Plotting in Association with R/qtl

Description

plotGeneModel Using an annotated vcf and gff file, plot the gene model with mutations.

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, makePlot = TRUE,
  returnData = TRUE)

Arguments

gff	A gene annotation in gff / gff3 format
snpEffVCF	A simple vcf file that has been annotated by the SNPeff program
geneID	The gff / vcf id of the gene of interest
upstreamBuffer	How far upstream of the gene should be plotted / extracted?
downstreamBuffer	How far downstream of the gene should be plotted / extracted?
features2plot	What features (in the gff) should be plotted?
colors	What colors should the features be?
mutations2annotate	What types of mutations should be annoted in the plot? These keywords must appear in the "INFO" column of the vcf file
pchMutation	What shape should the annotations be?
colMutation	What color should the annotations be?
orientation	What is the orientation of the gene? If NULL, determined from the gff.
windowSize	What window size should be used in the mutation sliding window plot?
stepSize	What step size should be used in the mutation sliding window plot?
scaleBar	Should a scale bar be plotted?

Value

A data.frame containing all mutations in the plot.

jtlovell/qtlTools documentation built on May 20, 2019, 3:14 a.m.