viRome_ggplot2

Legacy R code for the R package viRome modified to use ggplot2 for printing in the position.barplot and barplot.bam functions.

Install packages:

install.packages(c("BiocManager","Rcpp","seqinr","plyr","gsubfn","Rsamtools","reshape2","seqLogo", "motifStack", "S4Vectors", "ggplot2"))

BiocManager::install("seqLogo")
BiocManager::install("motifStack")

Load the libraries

library("seqinr")
library("plyr")
library("gsubfn")
library("Rsamtools")
library("reshape2")
library("seqLogo")
library("motifStack")
library("S4Vectors")
library("Rcpp")

Load the code

source("https://raw.githubusercontent.com/mw55309/viRome_legacy/main/R/viRome_functions.R")

There is a BAM file and associated .bai file called "SRR389184_vs_SINV_sorted.bam" in the data directory of this repo. Download them as examples

Run viRome

infile <- "SRR389184_vs_SINV_sorted.bam"

bam <- read.bam(infile, chr="SINV")
# requires only the output of read.bam()
bamc <- clip.bam(bam)
# requires only the output of clip.bam()
bpl <- barplot.bam(bamc)
# requires only the output of barplot.bam()
ssp <- size.strand.bias.plot(bpl)
# requires only the output of clip.bam()
dm <- summarise.by.length(bamc)
sph <- size.position.heatmap(dm)
# requires only the output of summarise.by.length()
sbp <- stacked.barplot(dm)
# requires only the output of clip.bam()
# though one should alter minlen, maxlen
# and reflen
sir <- position.barplot(bamc)
# requires only the output of clip.bam()
sr <- sequence.report(bamc)
# requires only the output of clip.bam()
pwm <- make.pwm(bamc)
# requires only the output of make.pwm()
pmh <- pwm.heatmap(pwm)
# requires only the output of sequence.report()
rdp <- read.dist.plot(sr)

Citation

If you are using this tool or parts of it in your research, please cite the original publication and our paper:

Watson M, Schnettler E, Kohl A. viRome: an R package for the visualization and analysis of viral small RNA sequence datasets. Bioinformatics. 2013 Aug 1;29(15):1902-3. doi: 10.1093/bioinformatics/btt297. Epub 2013 May 24. PMID: 23709497; PMCID: PMC3712215.

Lumi Viljakainen, Matthias A. Fürst, Anna V. Grasse, Jaana Jurvansuu1, Jinook Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, Sylvia Cremer. Antiviral immune response reveals host-specific virus infections in natural ant populations *

*will be updated as soon as it is on www.biorxiv.org