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OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data.

Hu Y, Yan C, Hsu CH, Chen QR, Niu K, Komatsoulis GA, Meerzaman D - Cancer Inform (2014)

Bottom Line: Relationships among genomic features in different chromosome positions can be represented in the forms of polygons or curves.Utilizing the statistical and graphic functions in an R/Bioconductor environment, OmicCircos performs statistical analyses and displays results using cluster, boxplot, histogram, and heatmap formats.In addition, OmicCircos offers a number of unique capabilities, including independent track drawing for easy modification and integration, zoom functions, link-polygons, and position-independent heatmaps supporting detailed visualization.

View Article: PubMed Central - PubMed

Affiliation: Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20850, USA.

ABSTRACT

Summary: OmicCircos is an R software package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. Such variations can be displayed as scatterplot, line, or text-label figures. Relationships among genomic features in different chromosome positions can be represented in the forms of polygons or curves. Utilizing the statistical and graphic functions in an R/Bioconductor environment, OmicCircos performs statistical analyses and displays results using cluster, boxplot, histogram, and heatmap formats. In addition, OmicCircos offers a number of unique capabilities, including independent track drawing for easy modification and integration, zoom functions, link-polygons, and position-independent heatmaps supporting detailed visualization.

Availability and implementation: OmicCircos is available through Bioconductor at http://www.bioconductor.org/packages/devel/bioc/html/OmicCircos.html. An extensive vignette in the package describes installation, data formatting, and workflow procedures. The software is open source under the Artistic-2.0 license.

No MeSH data available.


Related in: MedlinePlus

Integration of circular plots by OmicCircos and clusters from R of TCGA breast cancer data. Circular tracks from outside to inside: genome positions by chromosomes (black lines are cytobands), CNVs in Basal, Her2, Luminal A (LumA) and Luminal B (LumB) subtypes with 15 samples in each track (red: gain; blue: loss), in the center, four clusters from principle component analysis (PCA) of the gene expression data with R packages in the bioconductor.
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Related In: Results  -  Collection


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f2-cin-13-2014-013: Integration of circular plots by OmicCircos and clusters from R of TCGA breast cancer data. Circular tracks from outside to inside: genome positions by chromosomes (black lines are cytobands), CNVs in Basal, Her2, Luminal A (LumA) and Luminal B (LumB) subtypes with 15 samples in each track (red: gain; blue: loss), in the center, four clusters from principle component analysis (PCA) of the gene expression data with R packages in the bioconductor.

Mentions: The circular plot from the OmicCircos package can be seamlessly integrated with other types of R statistical graphics. For example, Figure 2 illustrates CNV and gene-expression data for the four breast cancer subtypes: Basal, Her2, Luminal A (LumA) and Luminal B (LumB) with 15 samples in each group. CNVs for each subtype are represented in individual tracks. Principal component analysis (PCA) of gene-expression data for the four subtypes is represented in the center of the figure. Distinct patterns of arm-level CNV gain or loss are visible, eg, 5q loss in Basal, 16q loss in Luminal A/B, and 10p gain in Basal. More examples of circular plots generated using OmicCircos package are available in the package vignette. These show comparative genomic analyses, expression quantitative trait loci (eQTLs), protein-protein interactions (PPIs), and gene interactions within the context of pathways.


OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data.

Hu Y, Yan C, Hsu CH, Chen QR, Niu K, Komatsoulis GA, Meerzaman D - Cancer Inform (2014)

Integration of circular plots by OmicCircos and clusters from R of TCGA breast cancer data. Circular tracks from outside to inside: genome positions by chromosomes (black lines are cytobands), CNVs in Basal, Her2, Luminal A (LumA) and Luminal B (LumB) subtypes with 15 samples in each track (red: gain; blue: loss), in the center, four clusters from principle component analysis (PCA) of the gene expression data with R packages in the bioconductor.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3921174&req=5

f2-cin-13-2014-013: Integration of circular plots by OmicCircos and clusters from R of TCGA breast cancer data. Circular tracks from outside to inside: genome positions by chromosomes (black lines are cytobands), CNVs in Basal, Her2, Luminal A (LumA) and Luminal B (LumB) subtypes with 15 samples in each track (red: gain; blue: loss), in the center, four clusters from principle component analysis (PCA) of the gene expression data with R packages in the bioconductor.
Mentions: The circular plot from the OmicCircos package can be seamlessly integrated with other types of R statistical graphics. For example, Figure 2 illustrates CNV and gene-expression data for the four breast cancer subtypes: Basal, Her2, Luminal A (LumA) and Luminal B (LumB) with 15 samples in each group. CNVs for each subtype are represented in individual tracks. Principal component analysis (PCA) of gene-expression data for the four subtypes is represented in the center of the figure. Distinct patterns of arm-level CNV gain or loss are visible, eg, 5q loss in Basal, 16q loss in Luminal A/B, and 10p gain in Basal. More examples of circular plots generated using OmicCircos package are available in the package vignette. These show comparative genomic analyses, expression quantitative trait loci (eQTLs), protein-protein interactions (PPIs), and gene interactions within the context of pathways.

Bottom Line: Relationships among genomic features in different chromosome positions can be represented in the forms of polygons or curves.Utilizing the statistical and graphic functions in an R/Bioconductor environment, OmicCircos performs statistical analyses and displays results using cluster, boxplot, histogram, and heatmap formats.In addition, OmicCircos offers a number of unique capabilities, including independent track drawing for easy modification and integration, zoom functions, link-polygons, and position-independent heatmaps supporting detailed visualization.

View Article: PubMed Central - PubMed

Affiliation: Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20850, USA.

ABSTRACT

Summary: OmicCircos is an R software package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. Such variations can be displayed as scatterplot, line, or text-label figures. Relationships among genomic features in different chromosome positions can be represented in the forms of polygons or curves. Utilizing the statistical and graphic functions in an R/Bioconductor environment, OmicCircos performs statistical analyses and displays results using cluster, boxplot, histogram, and heatmap formats. In addition, OmicCircos offers a number of unique capabilities, including independent track drawing for easy modification and integration, zoom functions, link-polygons, and position-independent heatmaps supporting detailed visualization.

Availability and implementation: OmicCircos is available through Bioconductor at http://www.bioconductor.org/packages/devel/bioc/html/OmicCircos.html. An extensive vignette in the package describes installation, data formatting, and workflow procedures. The software is open source under the Artistic-2.0 license.

No MeSH data available.


Related in: MedlinePlus