RT Journal Article
SR Electronic
T1 MicroScope: magnifying interactive gene expression heatmaps with RShiny and JavaScript
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 034694
DO 10.1101/034694
A1 Bohdan B. Khomtchouk
A1 Vytas Dargis-Robinson
A1 James R. Hennessy
A1 Claes Wahlestedt
YR 2015
UL http://biorxiv.org/content/early/2015/12/28/034694.abstract
AB Motivation Large gene expression heatmaps (≥ 200 genes) are difficult to read: while general expression level patterns may be observed via hierarchical clustering, the identities of specific gene names become entirely unreadable at large scale. More importantly, current state-of-the-art heatmaps are entirely static and require programming skills to produce.Results We create a user-friendly web app to create heatmaps that are both dynamic and interactive. A few mouse clicks allows a user to generate a heatmap based on an input .csv file and proceed to dynamically navigate to any sector of the heatmap via zooming in and out to any specific region, cluster, or even single gene. In addition to magnification, MicroScope also allows users to hover the mouse pointer over any specific gene to show precise expression level details, as well as create row and column dendrograms with colored branches using simple button clicks. As such, MicroScope presents a significant advance in heatmap visualization technology over current standard protocols.Availability and implementation MicroScope is hosted online as an RShiny web app based on the D3 JavaScript library: https://microscope.shinyapps.io/microscope. The methods are implemented in R, and are available as part of the MicroScope project at: https://github.com/Bohdan-Khomtchouk/Microscope.Contact: b.khomtchouk{at}med.miami.edu