Published online 17 May 2016 Nucleic Acids Research, 2016, Vol. 44, Web Serverissue W147–W153 doi: 10.1093/nar/gkw419 Heatmapper: web-enabled heat mapping for all Sasha Babicki 1 , David Arndt 1 , Ana Marcu 1 , Yongjie Liang 1 , Jason R. Grant 1 , Adam Maciejewski 2 and David S. Wishart 1,2,3,* 1 Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada, 2 Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada and 3 National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, AB T6G 2M9, Canada Received February 01, 2016; Revised April 24, 2016; Accepted May 04, 2016 ABSTRACT Heatmapper is a freely available web server that al- lows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface. Unlike existing non-commercial heat map packages, which either lack graphical interfaces or are specialized for only one or two kinds of heat maps, Heatmapper is a versatile tool that allows users to easily create a wide variety of heat maps for many different data types and applications. More specifically, Heatmapper allows users to generate, cluster and visualize: (i) expression-based heat maps from transcriptomic, proteomic and metabolomic ex- periments; (ii) pairwise distance maps; (iii) correla- tion maps; (iv) image overlay heat maps; (v) latitude and longitude heat maps and (vi) geopolitical (choro- pleth) heat maps. Heatmapper offers a number of simple and intuitive customization options for facile adjustments to each heat map’s appearance and plot- ting parameters. Heatmapper also allows users to in- teractively explore their numeric data values by hov- ering their cursor over each heat map cell, or by us- ing a searchable/sortable data table view. Heat map data can be easily uploaded to Heatmapper in text, Excel or tab delimited formatted tables and the re- sulting heat map images can be easily downloaded in common formats including PNG, JPG and PDF. Heatmapper is designed to appeal to a wide range of users, including molecular biologists, structural biologists, microbiologists, epidemiologists, envi- ronmental scientists, agriculture/forestry scientists, fish and wildlife biologists, climatologists, geolo- gists, educators and students. Heatmapper is avail- able at http://www.heatmapper.ca. INTRODUCTION Thanks to rapid developments in data rendering and visual- ization software, heat maps have become increasingly popu- lar routes to display information-rich data in both two and three dimensions. The concept of a heat map appears to have emerged from the widespread use of pseudo-coloured surface temperature maps (generated via infrared thermog- raphy) that became available in the 1970s and 1980s. In thermography, infrared or thermal imaging cameras are used to detect heat variations over the surface of an ob- ject. These kinds of image-based thermal heat maps actu- ally frst emerged in the 1950s (1) and have since become widely used in various felds ranging from medical imaging, weather monitoring, building inspection and materials en- gineering. The extension of the thermal heat map concept to assist with visualizing non-thermal data occurred in 1991 when the actual term ‘heatmaps’ was coined and later trade- marked (2). Indeed, the frst non-thermal or ‘data-matrix’ heat maps were used to depict real time fnancial market information. Since then data-matrix heat maps have been used in a wide variety of applications from molecular bi- ology (gene and protein expression mapping), to structural biology (pairwise distance measurements), to epidemiology (disease outbreak monitoring), to environmental science (ocean salinity mapping), to climatology (mapping rain- fall levels), to urban planning (traffc density mapping) and even to politics (showing regional voter preferences). Broadly speaking heat maps fall into two classes: (i) image-based heat maps and (ii) data-matrix heat maps. Image-based heat maps display numerical information that is mapped over an image, an object or a geographic loca- tion. Examples of image-based heat maps include choro- pleth heat maps (3), geospatial heat maps, webpage ‘eye- scan’ heat maps and anatomical heat maps. On the other hand, data-matrix heat maps display numerical data in a pseudo-coloured tabular or matrix format. The data may be subsequently clustered using various measures of similarity or dissimilarity. Examples of data-matrix heat maps include gene/protein/metabolite expression heat maps, correlation heat maps, taxonomic heat maps and pairwise distance heat maps. * To whom correspondence should be addressed. Tel: +1 780 492 0383; Fax: +1 780 492 1071; Email: david.wishart@ualberta.ca C  The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com Downloaded from https://academic.oup.com/nar/article/44/W1/W147/2499381 by guest on 19 August 2022