R: Visualize and Process Output from 'VirusHunterGatherer'

# Visualize and Process Output from 'VirusHunterGatherer'

## Documentation for package ‘Virusparies’ version 1.1.0

- DESCRIPTION file
- Package README

## Help Pages

Virusparies-package | Virusparies Package
CombineHittables | CombineHittables: Combine hittables.
ExportVirusDataFrame | ExportVirusDataFrame: Export processed hittables and summary stats data frames
ExportVirusGt | ExportVirusGt: (Experimental) Export Graphical Tables
ExportVirusPlot | Export Virusparies Plots
get_plot_parameters | Internal function to set default title and cutoff in boxplot function
ImportVirusTable | ImportVirusTable: Import VirusHunterGatherer hittables into R
SummarizeViralStats | SummarizeViralStats: Generate summary stats outside of plot functions
VgConLenViolin | VgConLenViolin: Generate a Violinplot of contig length for each group (Gatherer only)
VhgAddPhylum | VhgAddPhylum: extract Phylum information
VhgBoxplot | VhgBoxplot: Generate box plots comparing E-values,identity or contig length (Gatherer only) for each virus group
VhgGetSubject | VhgGetSubject: Process and Count Viral Subjects within Groups
VhgIdenFacetedScatterPlot | VhgIdenFacetedScatterPlot: Create a scatter plot of Viral refseq identity vs. -log10 of viral refseq E-value.
VhgIdentityScatterPlot | VhgIdentityScatterPlot: Scatter plot for refseq identity vs -log10 of refseq E-value
VhgPreprocessTaxa | VhgPreprocessTaxa: preprocess ViralRefSeq_taxonomy elements
VhgRunsBarplot | VhgRunsBarplot: Generate a bar plot showing the number of data sets with unique runs found for each Virus group.
VhgRunsTable | VhgRunsTable: Generate a gt summary table of unique runs for each virus group
VhgSubsetHittable | VhgSubsetHittable: Filter VirusHunter and VirusGatherer hittables
VhgSumHitsBarplot | VhgSumHitsBarplot: Generate a bar plot showing the sum of reads/contigs for each virus family
VhgTabularRasa | VhgTabularRasa: Generate Custom Formatted Graphical Tables
Virusparies | Virusparies Package