the community site for and by developmental biologists

About: Joachimg

I am a chemist from training, with a strong interest in biology. Our lab develops genetically encoded fluorescent probes and biosensors for quantitative functional imaging with the overarching goal to unravel (G-protein) signalling networks in time and space in cells and tissues. You can follow me on twitter: @joachimgoedhart

Posts by Joachimg:

Visualizing data with R/ggplot2 – One more time

Posted by 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[…]

Visualizing data with R/ggplot2 – It’s about time

Posted by 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[…]

A better bar

Posted by on April 18th, 2018

After leaving the bar, what are we to do? I propose to move on to a better bar (and I hope that you will not be disappointed when you find out that I’m actually referring to an interval). In a previous blog I advocated the transparent presentation and reporting of data in graphs. It was[…]

A tribute to parrots

Posted by on April 5th, 2018

In a previous blog, I have disgraced parrots by associating them with P-values and discrediting them for their mechanic repetition. Nevertheless, I admire the vivid colours of these multifaceted birds. Here, I want to make it up by dedicating a pseudo-colour look-up table (LUT) to parrots. The images produced by fluorescence microscopy are best displayed[…]

Prevent p-value parroting

Posted by on February 1st, 2018

Recently, Nature published my correspondence “Dispense with redundant P values”. It highlights my concern that p-values are often calculated because “everybody does it”. This reminded me of the mechanical repetition that parrots are well-known for (footnote 1). Parroting of p-value reporting should stop and I suggest to only present a p-value in a figure if[…]

Converting excellent spreadsheets to tidy data

Posted by 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[…]

See for yourCelLf

Posted by on August 18th, 2017

See for yourCelLf “Forget the textbook picture” is what I proclaim when I teach master students in a course on Cell biology and Advanced Microscopy. Although the textbook is a fantastic resource for teaching, it largely fails to convey the complexity of cells, including their size, dynamics and structure. To fully appreciate the intricacies of[…]

Leaving the bar in five steps

Posted by on March 24th, 2017

Introduction Graphs (or charts or plots) are often used for the display and summary of data. They are essential tools for the communication of results in presentations or manuscripts. One particular type of graph, the bar graph, is often used to quantitatively compare (multiple) conditions. The earliest known example of a bar graph, dates from[…]