Circa gives you the power to create beautiful circos plots without writing a single line of code
Making circos plots is often time-consuming and frustrating, but it doesn’t have to be that way.
Circa is desktop software (for Mac, Windows, and Linux) that allows you to make circos plots from your genomic data. You can load in genomic data, construct a circos plot, export as a PNG (image) and SVG (for publication), and save your session for later to continue constructing the perfect circos plot. Any type of genomic data with chromosome names and positions can be plotted with Circa.
Watch how you can make this circos plot in just 1 minute:
Or make this plot in 2 minutes:
Circa got a nice upgrade this year, see the new features in action here:
Ideal data for plotting in Circa includes variant calls, copy number profiles, and any genomic features like repeats, genes, or the plethora of data available in ENCODE or through the UCSC genome browser. Any file where the data is in rows and headers will work, including but not limited to: CSV, TSV, BED, BEDPE, VCF (specially parsed to expand the INFO field), and GTF.
— Basil Khuder (@basilk_) April 30, 2017
Papers citing Circa
The primary transcriptome, small RNAs, and regulation of antimicrobial resistance in Acinetobacter baumannii, BioRxiv. Beautiful Circa plot in Figure 1.
Integrated miRNA-mRNA spatial signature for oral squamous cell carcinoma: a prospective profiling study of Narrow Band Imaging guided resection, Nature Scientific Reports. Great use of multiple Circa track types in Figure 5.
High‐density genetic map using whole‐genome re‐sequencing for fine mapping and candidate gene discovery for disease resistance in peanut, Plant Biotechnology. 3 different Circa plots!
Circa also works with bacterial genomes
Check out this 5-minute video that illustrates how to make a complicated circos plot comparing two bacterial genomes (Escherichia coli and Salmonella tiphymurium) with 3 different datasets.
Circa can plot any genomic data from any organism and any reference genome. All you have to do is give Circa a file that says how long the chromosomes are. Files for human reference genomes hg19 and hg38 are included in Circa’s starter pack. It also includes instructions for getting chromosome names and sizes from other species through the UCSC genome browser.
There is no limit to the number of tracks or datasets you can plot in Circa.
You can add multiple plots on top of each other. Each track can contain multiple layers, which means you can put a scatter plot and a line chart on top of each other, and it will automatically rescale to accommodate both datasets. You can also set multiple horizontal lines, so thresholds like y=0, y=100, and y=1000 can be set with different colors. If you need vertical lines, you can use a rectangle layer to draw them, making it easy to draw several at once.
Several ways to plot your data
Use the ribbons layer to show when entire regions are related
Save and share your Circa plots
You can share circa plots with other people. When you save a plot, it generates a .circa file that includes everything your collaborator needs to see and edit the plot in Circa on their own computer. Just like Word or Photoshop files, if your colleague also has Circa on her computer, she can edit your plot, add data to it, restyle it, and export new images.
Flexible styling of plot elements
You can specify the chromosome colors however you like, using the easy color picker or by entering a list of HEX codes. When you have the perfect color scheme, you can copy the list of Hex codes as text to quickly apply the same colorscale to other figures in your paper.
Data file requirements
Data files you load into Circa must be smaller than 10 MB and be in a neat row and column format where columns are separated by tabs, commas, or spaces. Each file must have a header in the first row that you will use when deciding which columns to plot, and there must be columns corresponding to chromosome names and positions. VCF files are also supported (must have .vcf extension). Check the input file format tutorial for an in-depth walkthrough of the supported file types.
Export as PNG or SVG
PNG (.png) is a simple image format that can be opened with any image-editing application. Use this for the first submission to a journal or for sharing results in a talk.
SVG (.svg) is a specialized format that can be opened and edited with applications like Adobe Illustrator or Inkscape. It is a vector format, so the resolution is infinite. This is what journals often want to see for final submissions and will make your figure look crisp no matter how far people zoom in.
Circa version 1.2 came out in August, 2018, and with it comes some great new features for creating beautiful, detailed circos plots even faster and more easily than before:
Learn more about Circa
“Can I use Circa to plot _____?”
Circa works smoothly with genomic data from any species, and it doesn’t have any required built-in reference genomes or annotations of any kind, which means that it is completely flexible to anything with chromosomes.
What if I’m not plotting chromosomes?
You may be looking to draw another kind of circos plot called a “chord diagram“, which is what our other software Chordial is designed for. Chordial is built a lot like Circa, so it is also a desktop program and very easy to use.
Telling Circa about your reference genome(s)
Circa works with everything from human to plants to bacteria, and you can even use it for metagenomics or multiple bacterial genomes. All you have to do is give Circa a file that contains the names and sizes of the chromosomes:
chromosome,size 1,249250621 2,243199373 ... Y,59373566
Plotting small genomes
For plotting a single bacterial genome, plasmid, chloroplast or mitochondrial genome, just load a simple file like this as your reference genome:
Then you just have to make a column in your other datasets you want to plot that contains “my_genome” and set that as the chromosome for every layer you plot. If you have more than one of those small genomes, just add each of them with their sizes on a new line. Then make sure to use the same “chromosome” names from the reference file to refer to them across all your data files.
Transforming data into genomic coordinates
Circa needs all your data to have genomic coordinates. This means that all your datasets have to have columns that refer to chromosomes and positions within those chromosomes for plotting. If you want to do something different from this straight-forward genomic coordinate plotting, you will need to wrangle the data into the right format first. Check out the input files tutorial to understand these formats better and the data wrangling episode for help getting your data into one of those formats.
Questions? Check out these video tutorials
Note that new features are not included in these yet, stay tuned for videos showing the new features coming out in the next few weeks.
What you get
When you buy Circa, you will get immediate access to download Circa for Mac, Windows, and Linux operating systems. You will also get a Starter Pack of example input files, including the chromosome name and size files for human hg19 and hg38, which you will need to start a Circa plot. These are the same “genome” files you need for bedtools, and are very simple to make. The starter pack also includes instructions about how these files were downloaded from the UCSC genome browser, so you can use Circa for any organism you are working on.
If you have any questions about Circa, check out the FAQ and tutorials. If you still have a burning question, you can email me at firstname.lastname@example.org.