the community site for and by developmental biologists
the community site for and by developmental biologists
Posted by Joachim Goedhart on April 27th, 2020
Data from time-lapse experiments is often displayed in a graph or plot, to visualize the dynamics of biological systems (Goedhart, 2020). Ironically, the perception of the dynamics is largely lost in a static plot. That’s where animated plots come in. Animated plots are a great way to display the dynamics of the underlying data. Below, I[…]
Posted by Joachim Goedhart on June 25th, 2019
In a previous blog, I have highlighted several ways to visualize the cell-to-cell heterogeneity from time-lapse imaging data. However, I have ignored that data is often rescaled in a way that reduces variability. For time-lapse imaging data, it is common to set the initial fluorescence intensity to 1 (or 100%). As a consequence, any changes[…]
Posted by Joachim Goedhart on December 12th, 2018
When we examined the kinetics of Rho GTPase activity in endothelial cells in response to receptor stimulation (Reinhard, 2017), we noticed considerable cell-to-cell heterogeneity. In the original work we published graphs with the average response, reflecting the response of the whole cell population. However, these graphs fail to show the cellular heterogeneity. What is the[…]
Posted by Joachim Goedhart on October 8th, 2018
Calculation and reporting of p-values is common in scientific publications and presentations (Cristea and Ioannidis, 2018). Usually, the p-value is calculated to decide whether two conditions, e.g. control and treatment, are different. Although a p-value can flag differences, it cannot quantify the difference itself (footnote 1). Therefore, p-values fail to answer a very relevant question:[…]
Posted by Joachim Goedhart on June 26th, 2018
Experiments are rarely performed in isolation. Usually, several conditions are compared in parallel or sequential experiments. This experimental strategy also applies to time-dependent data, e.g. from timelapse imaging. So, naturally, after I published a ‘walk-through for plotting temporal data using R and ggplot2, I was immediately asked how to plot two (or more) sets of[…]
Posted by Joachim Goedhart on May 31st, 2018
The visualization of temporal data by line graphs has been documented and popularized by William Playfair in the 18th century (Aigner et al, 2011; Beniger and Robyn, 1978). Today, time-dependent changes are still depicted by line graphs and ideally accompanied by a measure of uncertainty (Marx, 2013). Below, I provide a ‘walk-through’ for generating such a[…]
Posted by Joachim Goedhart on October 6th, 2017
Structuring data according to the ‘tidy data‘ standard simplifies data analysis and data visualisation. But understanding the structure of tidy data does not come naturally (in my experience), since it is quite different from the structure of data in spreadsheets or tables. Here, I explain how to convert typical spreadsheet data to tidy data to[…]
