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HemI: a toolkit for illustrating heatmaps.

Deng W, Wang Y, Liu Z, Cheng H, Xue Y - PLoS ONE (2014)

Bottom Line: In addition, HemI provides multiple clustering strategies for analyzing the data.Publication-quality figures can be exported directly.We propose that HemI can be a useful toolkit for conveniently visualizing and manipulating heatmaps.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.

ABSTRACT
Recent high-throughput techniques have generated a flood of biological data in all aspects. The transformation and visualization of multi-dimensional and numerical gene or protein expression data in a single heatmap can provide a concise but comprehensive presentation of molecular dynamics under different conditions. In this work, we developed an easy-to-use tool named HemI (Heat map Illustrator), which can visualize either gene or protein expression data in heatmaps. Additionally, the heatmaps can be recolored, rescaled or rotated in a customized manner. In addition, HemI provides multiple clustering strategies for analyzing the data. Publication-quality figures can be exported directly. We propose that HemI can be a useful toolkit for conveniently visualizing and manipulating heatmaps. The stand-alone packages of HemI were implemented in Java and can be accessed at http://hemi.biocuckoo.org/down.php.

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Related in: MedlinePlus

Usage of HemI 1.0.(A) The numerical data in one of three file formats can be directly loaded, whereas the data area can be selected by dragging or holding-SHIFT-then-click manipulations. Titles for X-axis or Y-axis can also be specified; (B) Multiple options for manipulating the heatmp; (C) The numeric data can be clustered for either or both of X-axis and Y-axis; (D) Publication-quality figures can be exported, and two figure formats were supported.
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pone-0111988-g001: Usage of HemI 1.0.(A) The numerical data in one of three file formats can be directly loaded, whereas the data area can be selected by dragging or holding-SHIFT-then-click manipulations. Titles for X-axis or Y-axis can also be specified; (B) Multiple options for manipulating the heatmp; (C) The numeric data can be clustered for either or both of X-axis and Y-axis; (D) Publication-quality figures can be exported, and two figure formats were supported.

Mentions: First, the numerical data in one of the three file formats, including Microsoft Excel spreadsheet (.xls), Tab Separated Value (TSV) or Comma Separated Value (CSV) can be loaded through clicking on the “LOAD” button of the main interface. Then, users can select the numerical data area for visualizing a heatmap with mouse-dragging or holding-SHIFT-then-click manipulations. The titles for X-axis and Y-axis can be specified by inputting number of row and column in the data sheet (Figure 1A). For convenience, an “Auto Fill” button was provided, while the first column and row were regarded as the titles of Y-axis and X-axis, respectively. A heatmap will be automatically generated after clicking on the finish button.


HemI: a toolkit for illustrating heatmaps.

Deng W, Wang Y, Liu Z, Cheng H, Xue Y - PLoS ONE (2014)

Usage of HemI 1.0.(A) The numerical data in one of three file formats can be directly loaded, whereas the data area can be selected by dragging or holding-SHIFT-then-click manipulations. Titles for X-axis or Y-axis can also be specified; (B) Multiple options for manipulating the heatmp; (C) The numeric data can be clustered for either or both of X-axis and Y-axis; (D) Publication-quality figures can be exported, and two figure formats were supported.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4221433&req=5

pone-0111988-g001: Usage of HemI 1.0.(A) The numerical data in one of three file formats can be directly loaded, whereas the data area can be selected by dragging or holding-SHIFT-then-click manipulations. Titles for X-axis or Y-axis can also be specified; (B) Multiple options for manipulating the heatmp; (C) The numeric data can be clustered for either or both of X-axis and Y-axis; (D) Publication-quality figures can be exported, and two figure formats were supported.
Mentions: First, the numerical data in one of the three file formats, including Microsoft Excel spreadsheet (.xls), Tab Separated Value (TSV) or Comma Separated Value (CSV) can be loaded through clicking on the “LOAD” button of the main interface. Then, users can select the numerical data area for visualizing a heatmap with mouse-dragging or holding-SHIFT-then-click manipulations. The titles for X-axis and Y-axis can be specified by inputting number of row and column in the data sheet (Figure 1A). For convenience, an “Auto Fill” button was provided, while the first column and row were regarded as the titles of Y-axis and X-axis, respectively. A heatmap will be automatically generated after clicking on the finish button.

Bottom Line: In addition, HemI provides multiple clustering strategies for analyzing the data.Publication-quality figures can be exported directly.We propose that HemI can be a useful toolkit for conveniently visualizing and manipulating heatmaps.

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.

ABSTRACT
Recent high-throughput techniques have generated a flood of biological data in all aspects. The transformation and visualization of multi-dimensional and numerical gene or protein expression data in a single heatmap can provide a concise but comprehensive presentation of molecular dynamics under different conditions. In this work, we developed an easy-to-use tool named HemI (Heat map Illustrator), which can visualize either gene or protein expression data in heatmaps. Additionally, the heatmaps can be recolored, rescaled or rotated in a customized manner. In addition, HemI provides multiple clustering strategies for analyzing the data. Publication-quality figures can be exported directly. We propose that HemI can be a useful toolkit for conveniently visualizing and manipulating heatmaps. The stand-alone packages of HemI were implemented in Java and can be accessed at http://hemi.biocuckoo.org/down.php.

Show MeSH
Related in: MedlinePlus