VisualVariants

The goal of this project is to create an R package and executable scripts to visualize variants in variant call format (VCF) files and bcftools tab-delimited files.

Requirements

In order to run the VisualVariants, users need to install software, programming languages, and packages in their computing systems. The software, programming languages, and packages include:

R>=3.6.0

Installation

You can install the VisualVariants from Github with:

# Run this inside R environment
install.packages("devtools", dependencies = TRUE)
devtools::install_github("yenon118/VisualVariants")

# Run this in your terminal
git clone https://github.com/yenon118/VisualVariants.git

Usage

1. generateMissingVariantCountStackBarChartParallel.R

Rscript scripts/generateMissingVariantCountStackBarChartParallel.R [-h] [--cores CORES] --inputs INPUTS --output OUTPUT [--all]

mandatory arguments:
  --inputs INPUTS       Input bcftools tab delimited files
  --output OUTPUT       Output file path

optional arguments:
  -h, --help            show this help message and exit
  --cores CORES         Number of processing cores
  --all                 Output all files

2. generateSampleMissingPercentageScatterPlotParallel.R

Rscript scripts/generateSampleMissingPercentageScatterPlotParallel.R [-h] [--cores CORES] --inputs INPUTS --output OUTPUT [--all]

mandatory arguments:
  --inputs INPUTS       Input bcftools tab delimited files
  --output OUTPUT       Output file path

optional arguments:
  -h, --help            show this help message and exit
  --cores CORES         Number of processing cores
  --all                 Output all files

3. generateVariantCountHistogramParallel.R

Rscript scripts/generateVariantCountHistogramParallel.R [-h] [--cores CORES] --inputs INPUTS --output OUTPUT [--gap GAP] [--binwidth BINWIDTH]

mandatory arguments:
  --inputs INPUTS       Input bcftools tab delimited files
  --output OUTPUT       Output file path

optional arguments:
  -h, --help            show this help message and exit
  --cores CORES         Number of processing cores
  --gap GAP             Gap of ticks in the x axis
  --binwidth BINWIDTH   Width of each bin for the histogram

Examples

These are basic examples which show you how to use VisualVariants:

1. generateMissingVariantCountStackBarChartParallel.R

Rscript scripts/generateMissingVariantCountStackBarChartParallel.R \
--cores 3 \
--inputs /scratch/yenc/projects/VisualVariants/data/Nebraska.Chr01.txt \
--inputs /scratch/yenc/projects/VisualVariants/data/Nebraska.Chr02.txt \
--inputs /scratch/yenc/projects/VisualVariants/data/Nebraska.Chr03.txt \
--output /scratch/yenc/projects/VisualVariants/output/missing_variant_count_stack_bar_chart.png \
--all

2. generateSampleMissingPercentageScatterPlotParallel.R

Rscript scripts/generateSampleMissingPercentageScatterPlotParallel.R \
--cores 3 \
--inputs /scratch/yenc/projects/VisualVariants/data/Nebraska.Chr01.txt \
--inputs /scratch/yenc/projects/VisualVariants/data/Nebraska.Chr02.txt \
--inputs /scratch/yenc/projects/VisualVariants/data/Nebraska.Chr03.txt \
--output /scratch/yenc/projects/VisualVariants/output/sample_missing_percentage_scatter_plot.png \
--all

3. generateVariantCountHistogramParallel.R

Rscript scripts/generateVariantCountHistogramParallel.R \
--cores 3 \
--inputs /scratch/yenc/projects/VisualVariants/data/Nebraska.Chr01.txt \
--inputs /scratch/yenc/projects/VisualVariants/data/Nebraska.Chr02.txt \
--inputs /scratch/yenc/projects/VisualVariants/data/Nebraska.Chr03.txt \
--output /scratch/yenc/projects/VisualVariants/output/variant_count_histogram.png

Results

These are basic examples which show you how to use VisualVariants:

1. generateMissingVariantCountStackBarChartParallel.R

2. generateSampleMissingPercentageScatterPlotParallel.R

3. generateVariantCountHistogramParallel.R

Package Update

To upgrade VisualVariants to the latest version, please remove the package and re-install the latest VisualVariants package:

# Run this inside R environment
remove.packages("VisualVariants")
devtools::install_github("yenon118/VisualVariants")