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.
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
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
- 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
- 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
- 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
These are basic examples which show you how to use VisualVariants:
- 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
- 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
- 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
These are basic examples which show you how to use VisualVariants:
- generateMissingVariantCountStackBarChartParallel.R
- generateSampleMissingPercentageScatterPlotParallel.R
- generateVariantCountHistogramParallel.R
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")
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