Plotting Temporal Localization Part 6 - veeninglab/BactMAP GitHub Wiki

Now I use my new trajectory dataframe containing both DnaX and FtsZ data to plot the fluorescence localization over time using plotTracks(). You can use plotTracks() in multiple ways. First, I want to make a plot which has a similar layout as the kymographs, showing only the localization on the cell length axis over time. I can do this by putting the variable dimension to length in the plotting function.

The input I use here for plotTracks() is the mesh data myMesh and the trajectory data combo.

myTrackPlot <-
  plotTracks(myMesh, combo,
           tracks=TRUE,
           cell=4,
           mag="100x_DVMolgen",
           dimension="length")

myTrackPlot

The only thing which I still want to change is the colors. The standard colors which plotTracks() uses for mult-color tracks is the CUD colorblind-friendly palette. However, for this picture, I want the colors to match the viridis palettes of the Kymographs, so I selected two color values from the heatmaps using a color picker.

R recognizes hex-codes and a whole list of color names, so you can exchange what I put below for any of these (for instance, "burlywood1" or "cornflowerblue", if you wish).

reddish <- "#B63679FF"
greenish <- "#21908CFF"

Now I’ll use the ggplot2-function scale_color_manual() to change the color map. Note that I also flip the plot upside down to match it to the kymograph:

myTrackPlot + ggplot2::scale_color_manual(values=c("DnaX"=greenish, "FtsZ"=reddish)) +
  ggplot2::scale_y_reverse()