Tutorial Plotting Temporal Localization - veeninglab/BactMAP GitHub Wiki
Goal of the Tutorial
In this tutorial, we’ll recreate figure 5A-C from our preprint. In this figure, we’re investigating the movement of the replication fork during cell division and compare it’s localization to the localization of septum-protein FtsZ. We look at this using kymographs, cell towers and plotting the fluorescence trajectories over one or two spatial dimensions. To do this, we use a movie with DnaX-GFP & FtsZ-RFP in pneumococcus, imaged every 20 seconds.
In the follow-up of this tutorial, Custom Analysis, we’ll investigate the general movement of DnaX over time in a larger time-lapse analysis.
Note
Throughout this tutorial, I will use BactMAP, ggplot2-functions and basic R code to not only make the plots, but also adjust them, explore the data and save my datasets and plots. I will also give some motivation for why I do the analysis the way I do it. If you are just interested in the BactMAP plotting functions, you could skip through to the relevant sections in the content table below.
Contents
- Before Getting Started
- Data Import
- Making Kymographs
- Making Cell Towers
- Plotting Trajectories: Preparation
- Plotting Trajectories: One Dimension
- Plotting Trajectories: Two Dimensions
- Resources
| :arrow_left: Tutorials Overview | Plotting Temporal Localization Part 1: Before Getting Started :arrow_right: |
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