perc_Division: Filter timelapse data by growth speed and whether cells...

In vrrenske/shinyspots: Visualization and Analysis of Bacterial Cell Segmentation and Fluorescence Data

Filter timelapse data by growth speed and whether cells underwent a whole division cycle.

Description

The function takes timelapse dataframes including cell size, frame and cell ID and return a dataframe with information on growth speed, whether the cell underwent a full division (and how many divisions), and a binning of each cell division in percentages. Next to this, it gives a summary of the parameters in the input dataframe per binned division point. It also plots the individual cell growth over binned division, as well as the average cell growth.

Usage

perc_Division(timelapse, av = TRUE, plotgrowth = TRUE)

Arguments

timelapse	A dataframe from timelapse data containing at least the variables frame, cell and max.length.
av	When av==TRUE, the function returns a dataframe with the variables of the input dataframe averaged per binned division moment ("percentage_binned").
plotgrowth	When plotgrowth==TRUE, the function returns a plot of the cell growth by binned division point, growth speed and nth division.

Details

This function estimates whether a division is a "full" division by a set of cutoffs. In some cases, the segmentation data gives this information already. When this is the case, it can be more straightforward to use this data instead of this function.

Value

1. A dataframe timelapse containing the following variables on top of the variables already in the input dataframe:

division	the nth division in the timelapse this cell is making
min_frame	the frame number where this division starts
max_frame	the frame where the cell is dividing
av_length	the mean cell length over the whole division
length_var	the variance of the cell length during the whole division
division_time	the time this division takes (in frames)
fulldivision	indicates whether the division is a full division (1 = full)
coeff	the coefficient of the linear growth function of the cell for this division - indicator of growth speed
growth	the divisions are grouped in 4 groups: no growth ("none"), fast, medium and slow growth.
percentage	if the moment of cell birth is 0 and cell division is 100, the percentage gives how far the cell is from dividing at this moment
percentage_binned	percentage grouped in 10 groups, for averaging

2. A dataframe mean_by_percentage, where the variables are averaged over percentage_binned.

3. A ggplot plot_growth showing the cell size over the percentage of division.

4. A ggplot plot_avgrowth showing the average cell size over the percentage of division.

Author(s)

Renske van Raaphorst

Examples

## Not run: 
#this example won't have much meaning because the timelapse was quite short.
#but analysis is quick because the dataset is not very big:
#for a better example, download our DnaX dataset from veeninglab.com/bactmap

#Download FtsZ_tracks.rda from https://veeninglab.com/f/example_datasets.zip

load("FtsZ_tracks.rda")

percD <- perc_Division(FtsZ_tracks)

percD$plot_avgrowth

## End(Not run)

vrrenske/shinyspots documentation built on Oct. 28, 2023, 12:26 p.m.