In AnzaGhaffar/GT-Plotting: Visualize VCF Genotypes

knitr::opts_chunk$set(echo = TRUE)

Functions for plotting the genotypes from a vcf file.

Installation

You can install the released version of SorghumTestingData from Github with:

devtools::install_github("AnzaGhaffar/GT-Plotting")
install.packages("GTPlotting")
library(GTPlotting)

Functions

We will have access to three functions:

VcfToTable

vcf_testdata<-VcfToTable('vcffilename')

This function takes as input a vcf file with extension vcf or vcf.gz and creates an object which consists of 2 data frames

vcf_testdata$vcfdata

The vcfdata is the data frame which has the important features extracted from the vcf file for the genotype plotting

vcf_testdata$chromlen

This data frame has the chromosome names and the size of each chromosome.

GTPlotting_Chromosome

GTPlotting_Chromosome(vcf_testdata$vcfdata,vcf_testdata$chromlen,'Grinkan_CTRL')

This function plots the genotype of each chromosome, it takes three inputs the vcf data frame generated by the VcfToTable function, the chromosome length table generated by the VcfToTable function and the name of the control sample should be same as in the vcf file.

GTPlotting_Chromosome_Combined

GTPlotting_Chromosome_Combined(vcf_testdata$vcfdata,vcf_testdata$chromlen)

This function plots the genotype of all the chromosomes, it takes two inputs the vcf data frame generated by the VcfToTable function, the chromosome length table generated by the VcfToTable function.

AnzaGhaffar/GT-Plotting documentation built on July 16, 2020, 11:10 p.m.