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Visualization of proteomics data using R and bioconductor.

Gatto L, Breckels LM, Naake T, Gibb S - Proteomics (2015)

Bottom Line: Visualization is also of paramount importance as a form of communicating data to a broad audience.Here, we provided a short overview of the application of the R software to the visualization of proteomics data.We present a summary of R's plotting systems and how they are used to visualize and understand raw and processed MS-based proteomics data.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Department of Biochemistry, Computational Proteomics Unit, University of Cambridge, Cambridge, UK.

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Visualization of raw mass spectrometry data. See text for details. The top figures use the lattice package while the rest have been produced using the traditional graphics infrastructure.
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fig03: Visualization of raw mass spectrometry data. See text for details. The top figures use the lattice package while the rest have been produced using the traditional graphics infrastructure.

Mentions: Several packages, such as Rgraphviz [47], graph [48], RBGL [49], and igraph [50], also allow the user to manipulate, perform computations on and plot graphs. It is also possible to produce 3D figures in R using, for example, the rgl package [51], which also allows reorientation of the figure on the interactive plotting display (see e.g. Fig. 3). It is also possible to create animations in R with the animation package [52]. In the vignette, we display animated 3D plots of the raw MS data.


Visualization of proteomics data using R and bioconductor.

Gatto L, Breckels LM, Naake T, Gibb S - Proteomics (2015)

Visualization of raw mass spectrometry data. See text for details. The top figures use the lattice package while the rest have been produced using the traditional graphics infrastructure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4510819&req=5

fig03: Visualization of raw mass spectrometry data. See text for details. The top figures use the lattice package while the rest have been produced using the traditional graphics infrastructure.
Mentions: Several packages, such as Rgraphviz [47], graph [48], RBGL [49], and igraph [50], also allow the user to manipulate, perform computations on and plot graphs. It is also possible to produce 3D figures in R using, for example, the rgl package [51], which also allows reorientation of the figure on the interactive plotting display (see e.g. Fig. 3). It is also possible to create animations in R with the animation package [52]. In the vignette, we display animated 3D plots of the raw MS data.

Bottom Line: Visualization is also of paramount importance as a form of communicating data to a broad audience.Here, we provided a short overview of the application of the R software to the visualization of proteomics data.We present a summary of R's plotting systems and how they are used to visualize and understand raw and processed MS-based proteomics data.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Department of Biochemistry, Computational Proteomics Unit, University of Cambridge, Cambridge, UK.

Show MeSH