GenomeGraphs: integrated genomic data visualization with R

Abstract

Background: Biological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses.

Results: We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system.

Conclusion: GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R.

Figure 1

ArrayCGH and exon array data. The first track in this figure shows an ideogram of the human chromosome 3. The red marker highlights the plotted genomic region. The second track shows exon array data, where each data point corresponds to a probe measuring the expression level of an exon. The third track displays copy number data in green and segmented copy number data with dashed blue lines. Note the amplification which can be seen in both the copy number and exon array tracks, suggesting that the amplification event results in higher expression levels of the gene in this region. The bottom track shows the gene annotation data from Ensembl.

Figure 2

Transcript isoforms and exon array data. Probe-level exon array data is plotted in the top graphic. The data of the exon array is intentionally not plotted on the exact chromosomal location of the probes in order to clearly visualize alternative splicing events. Each line in the top track represents a different sample. Usually, there are four probes per exon on the Affymetrix GeneChip^® Human Exon 1.0 ST platform, vertical gray lines group these four probes belonging to the same exon together. The blue connecting lines map these exons to gene models as defined by Affymetrix (green) and Ensembl (orange). Transcript isoforms known for this gene are plotted in dark blue. The region highlighted in the plot by an RectangleOverlay object shows the exon that is not expressed in the samples. One can see that this is a known alternatively spliced exon as annotated by Ensembl.

Figure 3

Short read sequencing and tiling array data. Data plotted are Illumina sequencing data from Nagalakshmi et al. [9], tiling array data from David et al. [10], nucleosome data from Lee et al. [11], and conservation track data from Siepel et al. [12]. The semi-transparent box highlights a possible annotation error in SGD, as suggested by the occurrence of the transcript in multiple separate datasets. In addition, the conservation track data demonstrate corroborating evidence for the possibility of a longer gene.