- What is
- A programmable genome browser environment
- Genome broswer concepts
- A genome browser is a visulalization tool for plotting different types of genomic data in separate tracks along chromosomes.
ggbiopackage (Yin et al., 2012) facilitates plotting of complex genome data objects, such as read alignments (SAM/BAM), genomic context/annotation information (gff/txdb), variant calls (VCF/BCF), and more. To easily compare these data sets, it extends the faceting facility of
ggplot2to genome browser-like tracks.
- Most of the core object types for handling genomic data with R/Bioconductor are supported:
VCF, etc. For more details, see Table 1.1 of the
ggbio’s convenience plotting function is
autoplot. For more customizable plots, one can use the generic
- Apart from the standard
ggbiodefines serval new components useful for genomic data visualization. A detailed list is given in Table 1.2 of the vignette here.
- Useful web sites:
Tracks: aligning plots along chromosomes
Plotting genomic ranges
GRanges objects are essential for storing alignment or annotation ranges in R/Bioconductor. The following creates a sample
GRanges object and plots its content.
Circular genome plots
More complex circular example
Alignments and variants
To make the following example work, please download and unpack this data archive containing GFF, BAM and VCF sample files.
autoplot demo here
Additional genome graphics
RCircos(Zhang et al., 2013)
Genome Browser: IGV
View genome data in IGV
- Download and open IGV
- Select in menu in top left corner A. thaliana (TAIR10)
- Upload the following indexed/sorted Bam files with
File -> Load from URL...
- To view area of interest, enter its coordinates
Chr1:49,457-51,457in position menu on top.
Create symbolic links
For viewing BAM files in IGV as part of
systemPipeR: utilities for building NGS analysis pipelines
Controlling IGV from R
Note this may not work on all systems.