Plotting Temporal Localization part 7 - veeninglab/BactMAP GitHub Wiki

You can also use plotTracks() to plot the localization of DnaX and FtsZ over both cell length & width. For this, you just have to change the variable dimension to c("length", "width"):

myTrackPlot_2 <-
  plotTracks(myMesh, combo,
           tracks=TRUE,
           cell=4,
           mag="100x_DVMolgen",
           dimension=c("length","width"))

myTrackPlot_2

You see that in this case, the same cell is plotted twice, once with the FtsZ tracks, once with the DnaX tracks. Time is displayed in the color scale. While it is a bit more difficult to follow tracks over time in this plot, I find it an intuitive way to get a feeling of the total displacement.

For my figure, I like both tracks to match the kymograph colors, therefore I’ll replot the FtsZ figure with a different color map using the argument timepalette_lines:

myTrackPlot_FtsZ <-
  plotTracks(myMesh, box_FtsZ,
             tracks=TRUE,
             cell=4,
             mag="100x_DVMolgen",
             dimension=c("length", "width"),
             timepalette_lines="magma")

myTrackPlot_FtsZ