Author Archives: Linh Ngo

How to read PCA biplots and scree plots

Principal component analysis (PCA) has been gaining popularity as a tool to bring out strong patterns from complex biological datasets. We have answered the question “What is a PCA?” in this jargon-free blog post — check it out for a simple explanation of how PCA works. In a nutshell, PCA… Read more »

Principal component analysis explained simply

As we are entering the era of Big Data, everyone and their moms seem to be talking about PCA. All the papers you read mention PCA (with lots of jargon, of course). Half of the seminars you’ve been to this month touch on PCA. Your boss/collaborators suggest trying PCA on… Read more »

How to compare box plots

Box plots, a.k.a. box-and-whiskers plots, are an excellent way to visualize differences among groups. They manage to carry a lot of statistical details — medians, ranges, outliers — without looking intimidating. But box plots are not always intuitive to read. How do you compare two box plots? The key information… Read more »

More on how to compare box plots

We showed a quick and easy way to compare box plots in previous post. Let’s dig deeper into what information you can use to compare two box plots. Overlapping boxes and medians It gets tricky when the boxes overlap and their median lines are inside the overlap range. As always,… Read more »

5 reasons you should use a violin graph

1. Violin graph is like box plot, but better Box-and-whisker plots are great. They show medians, ranges and variabilities effectively. They allow comparing groups of different sizes. They are super simple to create and read, so naturally, they are all over the place. But box plots can be misleading. They… Read more »

How to draw a modified box plot

Box plots, a.k.a box-and-whisker plots, are an excellent way to compare groups. They are intuitive: viewers can see samples’ medians, distribution, and variabilities with a quick glance. They allow comparing samples of different sizes; for example, a set of 50 data points with a set of 30. They don’t even… Read more »

Tracing origin of Atacama ‘alien’ skeleton: A PCA step-by-step example

They found Ata 15 years ago in a deserted Chilean town. She resembled no one on Earth. She had features that would make James Cameron immediately call his director of photography: angular skull, disproportionately large head, and slanted eyes. She was indeed featured in a documentary film about UFOs and… Read more »

Proportional Venn diagram in 1 minute with BioVinci

Venn diagram is an excellent tool to visualize the relationship among sets. Ideally, the sizes of the circles and their overlapping area should be proportional to the relationship they convey. It is, however, quite a challenge to create a proportional Venn diagram. No worries: With BioVinci, you can get this… Read more »

How to craft a figure legend for scientific papers

Writing a scientific paper? Preparing for publication? Making a poster for a conference tomorrow? Let’s face it: People will skim through the body text of your paper/poster, and only look at the figures. We all love figures. They catch eyes, they deliver information effectively, they highlight your results. Figures are… Read more »

How to build a hierarchical clustering heatmap with BioVinci?

Heatmap, heatmap everywhere. They are an intuitive way to visualize information from complex data. You see them showing gene expression, phylogenetic distance, metabolomic profiles, and a whole lot more. In this tutorial, we will show you how to perform hierarchical clustering and produce a heatmap with your data using BioVinci…. Read more »