Visualize and Process Output from 'VirusHunterGatherer'

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Documentation for package ‘Virusparies’ version 1.1.0

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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