bactKymo: Creates kymographs or demographs from pixel values & cell...

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

Creates kymographs or demographs from pixel values & cell dimensions.

Description

bactKymo() takes the output of extr_OriginalCells() and makes kymographs or demographs of them, depending on the chosen options. By default, all cells are used to make a demograph where the average fluorescence over the length axis of each cell is plotted, where all cells are ordered by cell length.

When 'timeD' is set to TRUE, bactKymo() makes kymographs of single cells. However, when 'percDiv' is set to true as well, bactKymo will make a kymograph of the average of all cell's fluorescence over their length axis, binning cells by the moment of division they are in (see perc_Division()).

Other settings which can be changes are the bin size (in how many groups is the average fluorescence intensity over the cell length calculated), whether the bins are placed such, that they represent the cell length at that moment (sizeAV=TRUE, takes more computing time), and when using a demograph, whether the extreme values are removed (cutoff_demograph).

The output will standardly be in the "viridis" color scale of the viridis package. However, this can be overwritten manually by adding a fill color scale to the plot.

To make computing time shorter while playing with the settings, it is possible to first prepare the kymographs using prepForKymo(). This is generally not necessary, but recommended when plotting single cell kymographs one by one.

Usage

bactKymo(originalCells,
          timeD = FALSE,
          dimension = "length",
          bins = 25,
          sizeAV = FALSE,
          cells = "all",
          prep = TRUE,
          percDiv = FALSE,
          cutoff_demograph = 0.975,
          mag,
          legend=TRUE)

Arguments

originalCells	The output of extr_OriginalCells, which combines TIFF data with mesh data.
timeD	if timeD==TRUE, the resulting kymographs will be sorted by time, not by cell length and will be made of single cells.
dimension	default="length", but when put to "width" the kymographs will average over cell width.
bins	the amount of bins the fluorescence intensity will be averaged over (per cell/time point)
sizeAV	when sizeAV==TRUE, the kymographs will reflect the cell length (or width) on the y axes. Default to FALSE because the computing time is faster when there is no sizing.
cells	default = "all". 'cells' is a numeric vector OR the word "all". When set to "all" ,all cells will be processed into a demograph (when timeD==FALSE) or a kymograph will be made of all cells (when timeD==TRUE). When a numeric vector of length 1 or more, the cells identified with the cell numbers in these vector will be processed into a demograph (when timeD == FALSE), or a kymograph will be made of all single cells (when timeD==TRUE). Finally, when only 1 cell number is identified, a kymograph will be made of this cell (when timeD == TRUE). It is not possible to make a plot of a single cell without time dimension.
prep	default = TRUE. Inside the function, the data will be prepared so it is possible to plot kymographs. Sometimes, when you want to run bactKymo() multiple times on the same dataset, it can save time to prepare the dataset only once. For this you can use the function prepForKymo() first and use the as the argument originalCells, while setting 'prep' to FALSE.
percDiv	this will call for perc_Division() and bin the average fluorescence over cell length (or width) in 10 groups, from just divided to almost dividing. It will, by default, plot all cells and only works with timelapse data.
cutoff_demograph	to make it easier to look at demographs of all cells, the highest 2.5 percent of the intensity values are removed from the demograph. set the cutoff to 1 to not remove anything, or put it lower to remove more values.
mag	magnification converter (see Pixels2um. If used, the pixel values will be converted to micron.
legend	when legend==TRUE, a legend will be shown on the right. when FALSE, the legend will be omitted.

Details

Many options are possible within bactKymo(). Make sure you set the time dimension & cells correctly! For examples, see the BactMAP wiki

Note that when you have an output of many plots, it is useful to use gridExtra::grid.arrange() to save all plots in a PDF, this makes the plots easier to investigate and saves loading time in between.

Value

One or multiple demographs/kymographs (see the details in arguments).

Author(s)

Renske van Raaphorst

Examples

## Not run: 

#download example dataset TurnedCell4 from https://veeninglab.com/f/example_datasets.zip

load("TurnedCell4.Rda")

#to plot a timelapse demograph of 1 cell:

kymo_cell4 <- bactKymo(originalCells = TurnedCell4, timeD=TRUE, sizeAV=TRUE)

#to change the color scheme:
OrangeHot <- getPalette("OrangeHot")
require(ggplot2)
kymo_cell4 + ggplot2::scale_fill_gradient2(low=OrangeHot[1], mid=OrangeHot[2], high=OrangeHot[3])


## End(Not run)

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