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gtrellis: an R/Bioconductor package for making genome-level Trellis graphics.

Gu Z, Eils R, Schlesner M - BMC Bioinformatics (2016)

Bottom Line: However, current software packages to produce Trellis graphics have not been designed with genomic data in mind and lack some functionality that is required for effective visualization of genomic data.In addition, gtrellis provides an extensible framework that allows adding user-defined graphics.The gtrellis package provides an easy and effective way to visualize genomic data and reveal high dimensional relationships on a genome-wide scale. gtrellis can be flexibly extended and thus can also serve as a base package for highly specific purposes. gtrellis makes it easy to produce novel visualizations, which can lead to the discovery of previously unrecognized patterns in genomic data.

View Article: PubMed Central - PubMed

Affiliation: Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.

ABSTRACT

Background: Trellis graphics are a visualization method that splits data by one or more categorical variables and displays subsets of the data in a grid of panels. Trellis graphics are broadly used in genomic data analysis to compare statistics over different categories in parallel and reveal multivariate relationships. However, current software packages to produce Trellis graphics have not been designed with genomic data in mind and lack some functionality that is required for effective visualization of genomic data.

Results: Here we introduce the gtrellis package which provides an efficient and extensible way to visualize genomic data in a Trellis layout. gtrellis provides highly flexible Trellis layouts which allow efficient arrangement of genomic categories on the plot. It supports multiple-track visualization, which makes it straightforward to visualize several properties of genomic data in parallel to explain complex relationships. In addition, gtrellis provides an extensible framework that allows adding user-defined graphics.

Conclusions: The gtrellis package provides an easy and effective way to visualize genomic data and reveal high dimensional relationships on a genome-wide scale. gtrellis can be flexibly extended and thus can also serve as a base package for highly specific purposes. gtrellis makes it easy to produce novel visualizations, which can lead to the discovery of previously unrecognized patterns in genomic data.

No MeSH data available.


Different layout styles by gtrellis.a Default style with all chromosomes sorted in karyotypic order and arranged in one row; (b) Standard Trellis layout in which all panels have the same width; (c) Optimized layout which arranges chromosomes with similar length into the same column; (d, e) Layouts for parallel visualization of three data tracks with chromosomes arranged in one row (d) or two rows (e); (f) Non-rectangular layout without vertical alignment of panels in different rows for compact arrangement of chromosomes. In each panel, red rectangles represent the length of the corresponding chromosomes
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Fig1: Different layout styles by gtrellis.a Default style with all chromosomes sorted in karyotypic order and arranged in one row; (b) Standard Trellis layout in which all panels have the same width; (c) Optimized layout which arranges chromosomes with similar length into the same column; (d, e) Layouts for parallel visualization of three data tracks with chromosomes arranged in one row (d) or two rows (e); (f) Non-rectangular layout without vertical alignment of panels in different rows for compact arrangement of chromosomes. In each panel, red rectangles represent the length of the corresponding chromosomes

Mentions: gtrellis provides a simple and flexible way to initialize the global Trellis layout. In the initialization step, panels corresponding to genomic categories are allocated to proper positions in the plotting area. Positions and style of the Trellis layout can be adjusted either as traditional style or as an improved style for efficient genome data visualization. Figure 1 illustrates several styles for the global layout that can be produced by gtrellis. To make a clear comparison between different layout styles, two long chromosomes (human chromosome 1 and 3) and two short chromosomes (human chromosome 20 and 21) are selected. Figure 1a is the default style in which all chromosomes are arranged in one row in karyotypic order, and the panel width is proportional to each chromosome’s length. Such one-row style layout is broadly used by a lot of packages that focus on genomic data analysis (e.g. showing genome-wide read coverage or copy number variation from whole genome sequencing data). However, the drawback is that with increasing number of chromosome, the plotting region for each chromosome will shrink, limiting the possible resolution of visualized features. Figure 1b illustrates a standard Trellis layout. It is obvious that there are huge empty areas in the panels of chromosome 20 and 21, which makes the layout inefficient. In Fig. 1c, the traditional Trellis layout is improved so that chromosomes with similar length are put in the same column, resulting in a much better usage of plotting space compared to Fig. 1a and b.Fig. 1


gtrellis: an R/Bioconductor package for making genome-level Trellis graphics.

Gu Z, Eils R, Schlesner M - BMC Bioinformatics (2016)

Different layout styles by gtrellis.a Default style with all chromosomes sorted in karyotypic order and arranged in one row; (b) Standard Trellis layout in which all panels have the same width; (c) Optimized layout which arranges chromosomes with similar length into the same column; (d, e) Layouts for parallel visualization of three data tracks with chromosomes arranged in one row (d) or two rows (e); (f) Non-rectangular layout without vertical alignment of panels in different rows for compact arrangement of chromosomes. In each panel, red rectangles represent the length of the corresponding chromosomes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC4835841&req=5

Fig1: Different layout styles by gtrellis.a Default style with all chromosomes sorted in karyotypic order and arranged in one row; (b) Standard Trellis layout in which all panels have the same width; (c) Optimized layout which arranges chromosomes with similar length into the same column; (d, e) Layouts for parallel visualization of three data tracks with chromosomes arranged in one row (d) or two rows (e); (f) Non-rectangular layout without vertical alignment of panels in different rows for compact arrangement of chromosomes. In each panel, red rectangles represent the length of the corresponding chromosomes
Mentions: gtrellis provides a simple and flexible way to initialize the global Trellis layout. In the initialization step, panels corresponding to genomic categories are allocated to proper positions in the plotting area. Positions and style of the Trellis layout can be adjusted either as traditional style or as an improved style for efficient genome data visualization. Figure 1 illustrates several styles for the global layout that can be produced by gtrellis. To make a clear comparison between different layout styles, two long chromosomes (human chromosome 1 and 3) and two short chromosomes (human chromosome 20 and 21) are selected. Figure 1a is the default style in which all chromosomes are arranged in one row in karyotypic order, and the panel width is proportional to each chromosome’s length. Such one-row style layout is broadly used by a lot of packages that focus on genomic data analysis (e.g. showing genome-wide read coverage or copy number variation from whole genome sequencing data). However, the drawback is that with increasing number of chromosome, the plotting region for each chromosome will shrink, limiting the possible resolution of visualized features. Figure 1b illustrates a standard Trellis layout. It is obvious that there are huge empty areas in the panels of chromosome 20 and 21, which makes the layout inefficient. In Fig. 1c, the traditional Trellis layout is improved so that chromosomes with similar length are put in the same column, resulting in a much better usage of plotting space compared to Fig. 1a and b.Fig. 1

Bottom Line: However, current software packages to produce Trellis graphics have not been designed with genomic data in mind and lack some functionality that is required for effective visualization of genomic data.In addition, gtrellis provides an extensible framework that allows adding user-defined graphics.The gtrellis package provides an easy and effective way to visualize genomic data and reveal high dimensional relationships on a genome-wide scale. gtrellis can be flexibly extended and thus can also serve as a base package for highly specific purposes. gtrellis makes it easy to produce novel visualizations, which can lead to the discovery of previously unrecognized patterns in genomic data.

View Article: PubMed Central - PubMed

Affiliation: Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.

ABSTRACT

Background: Trellis graphics are a visualization method that splits data by one or more categorical variables and displays subsets of the data in a grid of panels. Trellis graphics are broadly used in genomic data analysis to compare statistics over different categories in parallel and reveal multivariate relationships. However, current software packages to produce Trellis graphics have not been designed with genomic data in mind and lack some functionality that is required for effective visualization of genomic data.

Results: Here we introduce the gtrellis package which provides an efficient and extensible way to visualize genomic data in a Trellis layout. gtrellis provides highly flexible Trellis layouts which allow efficient arrangement of genomic categories on the plot. It supports multiple-track visualization, which makes it straightforward to visualize several properties of genomic data in parallel to explain complex relationships. In addition, gtrellis provides an extensible framework that allows adding user-defined graphics.

Conclusions: The gtrellis package provides an easy and effective way to visualize genomic data and reveal high dimensional relationships on a genome-wide scale. gtrellis can be flexibly extended and thus can also serve as a base package for highly specific purposes. gtrellis makes it easy to produce novel visualizations, which can lead to the discovery of previously unrecognized patterns in genomic data.

No MeSH data available.