R/seqplots-package.R

In seqplots: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

#' @docType package
#' @name seqplots
#' 
#' @title 
#' SeqPlots - An interactive tool for visualizing NGS signals and sequence 
#' motif densities along genomic features using average plots and heatmaps.
#' 
#' @description
#' SeqPlots is a tool for plotting next generation sequencing (NGS) based 
#' experiments' signal tracks, e.g. reads coverage from ChIP-seq, RNA-seq 
#' and DNA accessibility assays like DNase-seq and MNase-seq, over user 
#' specified genomic features, e.g. promoters, gene bodies, etc. It can 
#' also calculate sequence motif density profiles from reference genome. 
#' The data are visualized as average signal profile plot, with error estimates 
#' (standard error and 95% confidence interval) shown as fields, or as series 
#' of heatmaps that can be sorted and clustered using hierarchical clustering, 
#' k-means algorithm and self organising maps. Plots can be prepared using R 
#' programming language or web browser based graphical user interface (GUI) 
#' implemented using Shiny framework. The dual-purpose implementation allows 
#' running the software locally on desktop or deploying it on server. 
#' SeqPlots is useful for both for exploratory data analyses and preparing 
#' replicable, publication quality plots. Other features of the software 
#' include collaboration and data sharing capabilities, as well as ability 
#' to store pre-calculated result matrixes, that combine many sequencing 
#' experiments and in-silico generated tracks with multiple different features. 
#' These binaries can be further used to generate new combination plots on fly, 
#' run automated batch operations or share with colleagues, who can adjust 
#' their plotting parameters without loading actual tracks and recalculating 
#' numeric values. SeqPlots relays on Bioconductor packages, mainly on 
#' rtracklayer for data input and BSgenome packages for reference genome 
#' sequence and annotations.
#' 
#' @details
#' Useful links:
#' \itemize{
#'   \item Project web page: \url{https://github.com/Przemol/seqplots} 
#'   \item Online documentation: \url{http://przemol.github.io/seqplots/} 
#'   \item Project wiki: \url{https://github.com/przemol/seqplots/wiki} 
#'   \item Issue tracker: \url{http://github.com/przemol/seqplots/issues} 
#'   \item Bug reports: \url{http://github.com/przemol/seqplots/issues/new}
#' }
#' 
#' @references 
#' \strong{R project and Bioconductor:}
#' \itemize{
#'   \item R Core Team (2014). R: A language and environment for statistical
#'    computing. R Foundation for Statistical Computing, Vienna, Austria. URL
#'    \url{http://www.R-project.org/}. 
#'   \item Bioconductor: Open software development for
#'    computational biology and bioinformatics R. Gentleman, V. J. Carey, D. M.
#'    Bates, B.Bolstad, M.Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, and
#'    others 2004, Genome Biology, Vol. 5, R80.  URL
#'    \url{http://www.bioconductor.org/}. 
#'   \item RStudio and Inc. (2014). shiny: Web
#'    Application Framework for R. R package version 0.10.1.
#'    \url{http://shiny.rstudio.com/}.
#'   \item Other CRAN packages: digest,
#'    DBI,RSQLite, jsonlite, plotrix, fields, grid, kohonen, Cairo, parallel 
#'   \item Bioconductor packages: IRanges, BSgenome, Rsamtools, rtracklayer,
#'    GenomicRanges and Biostrings
#'   }
#'   
#' \strong{JavaScript and CSS}
#' \itemize{
#'   \item jQuery framework - \url{http://jquery.com}
#'   \item Bootstrap - \url{http://getbootstrap.com}
#'   \item DataTables, Table plug-in for jQuery - 
#'    \url{http://www.datatables.net}
#'   \item jQuery File Upload Plugin - 
#'    \url{https://github.com/blueimp/jQuery-File-Upload}
#'   \item jQuery throttle - 
#'    \url{http://benalman.com/projects/jquery-throttle-debounce-plugin/}
#'   \item jQuery Cookie Plugin - 
#'    \url{https://github.com/carhartl/jquery-cookie}
#'   \item Modernizer JS library - \url{http://modernizr.com}
#'   \item JavaScript Templates - 
#'    \url{https://github.com/blueimp/JavaScript-Templates}
#'   \item JavaScript Color Picker - \url{http://jscolor.com}
#'   \item md5-js - \url{https://github.com/wbond/md5-js}
#'   \item Font Awesome - \url{http://fortawesome.github.io/Font-Awesome}
#'   \item Google Fonts - \url{https://www.google.com/fonts}
#'   \item jQuery user interface - \url{http://jqueryui.com} (documentation)
#'   \item jquery.tocify.js: jQuery Table of Contents - 
#'    \url{https://github.com/gfranko/jquery.tocify.js} (documentation)
#'   \item Strapdown \url{https://github.com/arturadib/strapdown} 
#'    (documentation)
#'   \item Bootswatch themes - \url{http://bootswatch.com} (documentation)
#'   \item google-code-prettify - 
#'    \url{https://code.google.com/p/google-code-prettify} (documentation)
#'   \item marked - \url{https://github.com/chjj/marked} (documentation)
#' }
#' 
#' \strong{Important conceptual contribution to the project}
#' \itemize{
#' \item Liu T, Ortiz J, Taing L, Meyer C, Lee B, Zhang Y, Shin H, Wong S, Ma J,
#' Lei Y, et al. 2011. 
#' \href{http://www.ncbi.nlm.nih.gov/pubmed/21859476}{Cistrome: an integrative 
#' platform for transcriptional regulation studies.} Genome Biology 12: R83. 
#' \item Thomas Williams, Colin Kelley and others (2010).
#' Gnuplot 4.4: an interactive plotting program. URL 
#' \url{http://www.R-project.org/}. 
#' \item Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H.,
#' Zahler, A.M. and Haussler, a. D. (2002). 
#' \href{http://www.ncbi.nlm.nih.gov/pubmed/12045153}{The Human Genome Browser 
#' at UCSC}. Genome Research. 12:996-1006. 
#' \item Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D.
#' (2010). \href{http://www.ncbi.nlm.nih.gov/pubmed/20639541}{BigWig and BigBed:
#'  enabling browsing of large distributed datasets.} Bioinformatics.
#' 1;26(17):2204-7 
#' \item Nicol, J.W., Helt, G.A., Blanchard, S.G., Raja, A. and Loraine, A.E. 
#' (2009). \href{http://www.ncbi.nlm.nih.gov/pubmed/19654113}{The Integrated 
#' Genome Browser: free software for distribution and exploration of 
#' genome-scale datasets.} Bioinformatics (Oxford, England). 25:2730-1. 
#' \item Thorvaldsdottir, H., Robinson, J.T. and Mesirov, J.P. (2012). 
#' \href{http://www.ncbi.nlm.nih.gov/pubmed/22517427}{Integrative Genomics 
#' Viewer (IGV): high-performance genomics data visualization and
#' exploration.} Briefings in bioinformatics. bbs017 
#' }
#' 
#' \strong{Server deployment}
#' \itemize{
#'   \item Shiny Server - \url{https://github.com/rstudio/shiny-server}
#'   \item ShinyApps - \url{https://github.com/rstudio/shinyapps}
#' }
#' 
#' \strong{Publications containing figures made by SeqPlots}
#' \itemize{
#'   \item Chen RA, Stempor P, Down TA, Zeiser E, Feuer SK, Ahringer J. 
#'   \href{http://www.ncbi.nlm.nih.gov/pubmed/24653213}{Extreme HOT regions are 
#'   CpG-dense promoters in C. elegans and humans.} Genome Res 
#'   24(7):1138-1146 Jul 2014
#'} 
#' 
#' 
#' @author Przemyslaw Stempor
#' 
#' @import rtracklayer GenomicRanges BSgenome Biostrings IRanges GenomeInfoDb
#' @import DBI RSQLite parallel jsonlite
#' @import methods digest methods
#' @import ggplot2 reshape2 gridExtra DT RColorBrewer
#' @import Rsamtools GenomicAlignments
#' @importFrom fields image.plot set.panel imageplot.info imageplot.setup 
#' tim.colors poly.image
#' @importFrom grid textGrob gpar grid.draw
#' @importFrom kohonen supersom
#' @importFrom plotrix dispersion
#' @importFrom shiny runApp
#' @importFrom class somgrid
#' @importFrom S4Vectors recycleIntegerArg
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