Virusparies {Virusparies} | R Documentation |
Virusparies Package
Description
Virusparies designed for visualizing output from VirusHunterGatherer.
Details
VirusHunterGatherer is a pipeline designed for data-driven virus discovery (DDVD). It involves two steps: (i) Virushunter conducts sensitive homology-based detection of viral sequence reads in unprocessed data, identifying the most conserved regions of a virus, which serve as seeds for the (ii) Virusgatherer step that assembles full-length viral genome sequences.
The Virusparies package provides a set of plotting functions tailored for visualizing VirushunterGatherer hittables. The name draws inspiration from the hunter-gatherer metaphor, with "paries" derived from Latin meaning "wall". It symbolizes the parietal art left by ancient hunters and gatherers on walls, summarizing their stories and beliefs.
Functions
This package includes the following functions:
Import:
-
ImportVirusTable
: Import VirusHunterGatherer hittables into R.
VirusHunterGatherer Plots:
-
VhgBoxplot
: Box plot plotting refseq sequence identity, E-values or contig length for each group. -
VhgIdenFacetedScatterPlot
: Faceted scatter plot for reference sequence identity vs -log10 of reference E-value. -
VhgIdentityScatterPlot
: Scatter plot for reference sequence identity vs -log10 of reference E-value. -
VhgRunsBarplot
: Bar plot showing how many unique runs map against each virus. -
VhgSumHitsBarplot
: Bar plot for the sum of hits for each virus found in group.
VirusGatherer only plots:
-
VgConLenViolin
: Violin plot to visualize the distribution of contig lengths.
Graphical Tables(gt):
-
VhgRunsTable
: Generate a gt-table for VhgRunsBarplot. -
VhgTabularRasa
: Generate custome gt-tables.
Export:
-
ExportVirusDataFrame
: Export data frames. -
ExportVirusGt
: Export graphical tables. -
ExportVirusPlot
: Export plots.
Utils:
-
CombineHittables
: Combine hittables. -
SummarizeViralStats
: Generate summary stats outside of plot functions. -
VhgAddPhylum
: Extract phylum information. -
VhgGetSubject
: Process and Count Viral Subjects within Groups. -
VhgPreprocessTaxa
: Process ViralRefSeq_taxonomy column. -
VhgSubsetHittable
: Filter VirusHunterGatherer data based on user’s own criteria.
Author(s)
Maintainer: Sergej Ruff (serijnh@gmail.com)
Other contributors:
Chris Lauber (chris.lauber@twincore.de)
Li Chuin, Chong (lichuin.chong@twincore.de)
If you have any questions, suggestions, or issues, please feel free to contact Sergej Ruff (serijnh@gmail.com).
See Also
VirusHunterGatherer is available on: https://github.com/lauberlab/VirusHunterGatherer.
If you encounter any errors or issues, please report them at: https://github.com/SergejRuff/Virusparies/issues.