Plotting Temporal Localization Part 5 - veeninglab/BactMAP GitHub Wiki

Plotting Trajectories: Preparation

Connecting Tracked Fluorescence to Cell Segmentation Data

Another way to display the localization of proteins over time is by plotting the trajectories of fluorescent objects over time. I used iSBatch to track fluorescent spots/filaments and we already imported them as tracks_DnaX and tracks_FtsZ. To prepare this data for plotting, we need to connect the tracks to the cell outlines. We can do this using the function spotsInBox().

spotsInBox() is a function which is useful if your cell outline data comes from a different program than your fluorescence detection data. It’s sister function is objectsInBox(). It returns a list of dataframes, of which we will use spots_relative:

box_DnaX <- spotsInBox(tracks_DnaX, myMesh)$spots_relative

box_FtsZ <- spotsInBox(tracks_FtsZ, myMesh)$spots_relative

Combining FtsZ and DnaX data into one dataset

To plot both DnaX and FtsZ in the same plot, I combine both dataframes using the function combineDataframes(). This function takes the datasets you put in, puts them together and adds a column "condition" and/or "channel" to the data indicating which data belongs to which condition/channel. The main output of this function is called finalframe. In our case, we immediately take out this finalframe using the $-operator. Check the output of the code below using View(combo) and/or summary(combo).

combo <- combineDataframes(listofdataframes=list(box_DnaX, box_FtsZ),
                           listofchannels = list("DnaX", "FtsZ"))$finalframe

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