Data Visualization – Page 2 – IRIC's Bioinformatics Platform

Formatting data for Circos with R

When generating a Circos plot, the formatting of the data to be represented is a crucial step. Here are some pointers on how to avoid the dreadful *** CIRCOS ERROR ***. All data files must be in text format. For instance, using R, I would generate a myData.txt file that I would then call within a specific plot block (<plot>...</plot>). Data files are used for 2-dimensional graphical representations (histogram, scatter plot, heatmap, tiles), labels (which are technically also a type [...]

By Caroline|2017-04-29T15:36:21+00:00October 29, 2015|Categories: Data Visualization, R|Tags: Circos, data analysis, data manipulation|0 Comments

Draw me a Circos

How pretty would that look in my article? Very Pretty! As well as being informative! You might want to use a Circos for your own personal analysis or as an article figure. In both cases, this kind of representation is useful when it comes to visualizing data in a more global or complete manner: you can have multiple types of data ranging across various chromosomal sequences. However, as wonderful and exciting the idea of having your own personal Circos might [...]

By Caroline|2017-05-01T10:03:50+00:00August 20, 2015|Categories: Data Visualization|Tags: biology, Circos, genomic|0 Comments

Identifying a point in ggplot2

So you have spent much time converting your simple R plot to a full-fledged ggplot2 graph with all its bells and whistles just to find that you are unable to identify a point on this graph to further investigate it. Indeed, the typical identify method is not applicable to ggplot2 graphs. Fortunately, there is a solution, which involves performing all the work yourself by going under the hood of ggplot2 to access the low-level graphics system on which it is [...]

By Patrick|2017-05-01T10:13:03+00:00March 11, 2015|Categories: Data Visualization, R|Tags: ggplot2|0 Comments

Best practices in data visualization

Sébastien's last post presented a hard-to-understand graph. The Venn diagram with four sets is a good example of visualization gone wrong. Good practices in data visualization is a hot topic right now. Not just in science, but in multiple areas such as journalism and business intelligence. Indeed, the crowd was quite heterogeneous at the first Visualisation Montréal meeting in August where more than 100 persons showed up! And the free ebook that was launched at the meeting targets beginners from all fields. [...]

By Geneviève|2017-04-29T15:40:51+00:00October 31, 2014|Categories: Data Visualization|0 Comments

Venn diagrams: a visualization nightmare!

I was recently reading a paper (a very inspiring read mapper for RNA-Seq!). At some point the authors wanted to present the overlap between splice junctions detected by 4 RNA-Seq read mappers and choose to do so using the ubiquitous Venn diagram (see Fig. 1). I spent a few minutes staring at this colorful mosaic... without gaining much insight. Fig. 1: Example of a four-way Venn diagram. Reproduced from figure 4b of Genome Biology, 14(3):R30, 2013. Which mappers overlapped most in [...]

By Sébastien|2017-04-29T17:20:46+00:00October 20, 2014|Categories: Data Visualization, Statistics|1 Comment