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oppHeatmap: Rendering Various Types of Heatmaps for Omics Data

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Abstract

Heatmaps are preferred visualization modes for biologists to display high-dimensional information from high-throughput omics data. Many software including website services and R packages are available to generate various types of customized heatmaps. Here, we describe oppHeatmap (omics pilot platform of heatmap), a new tool constructed to render different kinds of heatmaps through MATLAB. oppHeatmap is available for plotting ordinary heatmaps, hierarchical clustering, TreeMaps, microplates graph, sample correlation (full heatmap and upper and lower triangle parts), gene correlation (between columns or tables), and polar heatmaps. oppHeatmap can support the modification of borders, fonts, and colors to customize the final plots. oppHeatmap can not only read data from Microsoft Excel to generate specific heatmaps but also make Excel heatmaps by coloring each cell in Excel. The graphs can be stored in SVG (supported vector graph) format and modified by other SVG recognition software. oppHeatmap is designed by MATLAB AppDesigner with GUI (graphical user interface) operation. The program for oppHeatmap was available at https://github.com/HangZhouSheep/oppHeatmap.are diagramed by

Graphical Abstract

All kinds of heatmaps oppHeatmap. The main function of oppHeatmap is to enable visualization of two types of heatmaps and a total of 11 graphs. The first type is a heatmap with a polar or rectangular coordinate system, including ordinary heatmap, microplates graph, polar heatmap, and Excel heatmap. The last one involves writing the heatmap in Excel and others in MATLAB. The second type is with rearranged rows and columns, which includes hierarchical clustering, TreeMaps, and sample/gene correlation between columns or rows. All plots support row standardization for better color contrast. Eleven base functions implement heatmap plotting in the command line environment of MATLAB. GUI designed by AppDesigner supports the interactive construction of heatmaps.

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Data Availability

The program of oppHeatmap was available at https://github.com/HangZhouSheep/oppHeatmap.

Abbreviations

oppHeatmap:

Omics pilot platform of heatmap

GUI:

Graphical user interface

HCA:

Hierarchical cluster analysis

HTML:

Hypertext markup language

SVG:

Supported vector graph

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Acknowledgements

We are so grateful for the selfless help from HSEN Biotech (Shanghai) Co., Ltd. for oppHeatmap maintenance.

Funding

This research was supported by the National Key R&D Program of China (2021YFF0703702) and the National Nature Science Foundation of China (32070605).

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Authors and Affiliations

  1. Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China

    Ze-ning Wang, Jun Yao, Hang Liu, Yang Liu, Hong Jin & Yang Zhang

Authors
  1. Ze-ning Wang
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  2. Jun Yao
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  3. Hang Liu
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  4. Yang Liu
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  5. Hong Jin
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  6. Yang Zhang
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Contributions

1. Conception and design: Yang Zhang.

2. Administrative support: Hong Jin and Yang Zhang.

3. Data analysis and interpretation: Zening Wang.

4. Program writing: Yang Zhang and Yang Liu.

5. Manuscript writing: Jun Yao and Hang Liu.

6. Final approval of manuscript: all authors.

Corresponding authors

Correspondence to Hong Jin or Yang Zhang.

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All authors consent to participate in the project.

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All authors consent to publish the paper.

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The authors declare no competing interests.

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Ze-ning Wang and Jun Yao contributed equally.

Supplementary Information

ESM 1

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Wang, Zn., Yao, J., Liu, H. et al. oppHeatmap: Rendering Various Types of Heatmaps for Omics Data. Appl Biochem Biotechnol 196, 2356–2366 (2024). https://doi.org/10.1007/s12010-023-04652-1

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