Overview of Plot Functions - veeninglab/BactMAP GitHub Wiki

In short, the included data visualization functions of BactMAP can be grouped in 3 categories:

1. Functions visualizing the fluorescence intensity values directly from uploaded microscopy images
2. Functions for the visualization of subcellular localizations
3. Functions specifically designed to visualize timelapse movies.

Plot the (raw) fluorescence

When using multiple programs to detect cell outlines or internal fluorescence, or when you want to compare the performance of different programs & algorithm, plotting them all next to each other can be very helpful. For this, you can use plotRaw() to do exactly that.

When you want to have an overview of the localization of your fluorescent protein over time in one cell, bactKymo() can do this for you. Apart from that, it is possible to plot the internal fluorescence in a group of cells ordered by cell length (demographs), or to bin cells of time-lapses by their division state.

Plot subcellular localization & compare conditions/channels

Most BactMAP plotting functions are made to visualize fluorescence localization (spots or objects) detected with segmentation or detection software inside the cell. The most general function, made for plotting the localization of fluorescent spots inside the cell, is createPlotList(). A similar function to this is plotObjects, which does the same for intercellular objects as filaments. Then, plotOverlay() can be used to plot datasets with multiple conditions and/or fluorescent channels.

Finally, plotTracks() is a function to plot the localization of fluorescent spots in cells over time.

Time lapse analysis

For time-lapses, there is the possibility to 1. plot the cell genealogy combined with the internal fluorescence using plotTreeBasic(), 2. group the cells by their growth speed using percDivision() and make single-cell movies using plotCellsTime().