An interactive tool for visualizing track signals and sequence motif densities along genomic features using average plots and heatmaps

❗ RELEASE NOTE ❗

GitHub repository holds development version of SeqPlots. The release is available on Bioconductor. Please report the problem, bugs, unexpected behaviors and missing features using issue tracker.

Live demo

The working demonstration preview of SeqPlots is available on ShinyApps.io: https://seqplots.shinyapps.io/seqplots/

Demo limits:

• the application contains some pre-loaded data (C. elegans genes and histone modifications)
• size of uploaded files is limited to 30MB, please bin or subset your tracks to fit within the limit (due to ShinyApps beta upload limitations)
• only C. elegans genome is available (due ShinyApps beta space limits)
• uploaded files will be deleted after some time

Introduction

The SeqPlots is universal, web browser based tool for plotting average track signal (e.g. reads coverage) and sequence motif density over user specified genomic features. The data are visualized on linear plot, with error estimates as fields, or as series of heatmaps that can be sorted and clustered. The dual-purpose implementation allows running the software locally on desktop or deploying it on server. The unique features of our software are 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.

Installation

Install develpment version from Bioconductor:

source("http://bioconductor.org/biocLite.R")
biocLite("seqplots")

To install GitHub vesrion (in order to solve dependencies install from Bioconductor first):

if (!require("devtools")) install.packages("devtools")
devtools::install_github('przemol/seqplots', build_vignettes=FALSE)

Quick start

To start web browser GUI:

library(seqplots)
run()

To start with R scripting mode:

?getPlotSetArry

Mac OS X bundle app

Mac OS X bundle is an easy way to use SeqPlots for Mac OS X users. It contains R binaries pre-installed Bioconductor dependencies. Additionally, the reference genome for Caenorhabditis elegans is included. The sequences for other popular model organisms can be downloaded using graphical user interface.

Download the current version here: https://github.com/Przemol/seqplots_osx/releases/latest

The bundle requires OS X 10.6 (Snow Leopard) and above with X11 installed. X11 was included with OS X up to version 10.7 (Lion). OS X 10.8 (Mountain Lion) and above require installation of Xquartz package, see more here: http://support.apple.com/en-us/HT201341

References

R project and Bioconductor

• R Core Team (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
• 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 http://www.bioconductor.org/.
• RStudio and Inc. (2014). shiny: Web Application Framework for R. R package version 0.10.1. http://shiny.rstudio.com/
• Other CRAN packages: digest, DBI,RSQLite, RJSONIO, plotrix, fields, grid, kohonen, Cairo and parallel
• Bioconductor packages: IRanges, BSgenome, Rsamtools, rtracklayer, GenomicRanges and Biostrings

JavaScript and CSS

• jQuery framework - http://jquery.com
• Bootstrap - http://getbootstrap.com
• DataTables, Table plug-in for jQuery - http://www.datatables.net
• jQuery File Upload Plugin - https://github.com/blueimp/jQuery-File-Upload
• jQuery throttle - http://benalman.com/projects/jquery-throttle-debounce-plugin/
• jQuery Cookie Plugin - https://github.com/carhartl/jquery-cookie
• Modernizer JS library - http://modernizr.com
• JavaScript Templates - https://github.com/blueimp/JavaScript-Templates
• JavaScript Color Picker - http://jscolor.com
• md5-js - https://github.com/wbond/md5-js
• Font Awesome - http://fortawesome.github.io/Font-Awesome
• Google Fonts - https://www.google.com/fonts
• jQuery user interface - http://jqueryui.com (documentation)
• jquery.tocify.js: jQuery Table of Contents - https://github.com/gfranko/jquery.tocify.js (documentation)
• Strapdown https://github.com/arturadib/strapdown (documentation)
• Bootswatch themes - http://bootswatch.com (documentation)
• google-code-prettify - https://code.google.com/p/google-code-prettify (documentation)
• marked - https://github.com/chjj/marked (documentation)

Important conceptual contribution to the project

• Liu T, Ortiz J, Taing L, Meyer C, Lee B, Zhang Y, Shin H, Wong S, Ma J, Lei Y, et al. 2011. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biology 12: R83.
• Thomas Williams, Colin Kelley and others (2010). Gnuplot 4.4: an interactive plotting program. URL http://www.R-project.org/.
• Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M. and Haussler, a. D. (2002). The Human Genome Browser at UCSC. Genome Research. 12:996–1006.
• Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. (2010). BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 1;26(17):2204-7
• Nicol, J.W., Helt, G.A., Blanchard, S.G., Raja, A. and Loraine, A.E. (2009). The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics (Oxford, England). 25:2730–1.
• Thorvaldsdóttir, H., Robinson, J.T. and Mesirov, J.P. (2012). Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in bioinformatics. bbs017

Server deployment

• Shiny Server - https://github.com/rstudio/shiny-server
• ShinyApps - https://github.com/rstudio/shinyapps

Publications containing figures made by SeqPlots

• Chen RA, Stempor P, Down TA, Zeiser E, Feuer SK, Ahringer J. Extreme HOT regions are CpG-dense promoters in C. elegans and humans. Genome Res 24(7):1138-1146 Jul 2014