prepForKymo: Prepare whole dataset for single cell kymographs.

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

Prepare whole dataset for single cell kymographs.

Description

Extension from bactKymo, this function prepares a dataset for kymograph plotting. Recommended if you plan to plot a lot of kymographs from one dataset one by one; this will speed up the process. If you don't plan to do this, use bactKymo immediately.

Usage

prepForKymo(turnedCells, dimension = "length", bins = 25, sizeAV = FALSE)

Arguments

turnedCells	Output from extr_OriginalCells, which includes the pixel values (of the fluorescence signal) in each cell.
dimension	Default = "length", "width" is also possible. This decides on which dimension the kymograph will be calculated.
bins	Default = 25. The amount of bins in which the average fluorescence over length or width will be calculated.
sizeAV	When sizeAV == TRUE, the bins are placed along the y axis of the plot according to cell size. This takes more computation time.

Value

A dataframe suitable for bactKymo().

Examples

## Not run: 
#download & unzip https://veeninglab.com/f/examples.zip and set the path to the downloaded folder.

load("TurnedCell4")
prepForKymo(TurnedCell4)

## End(Not run)

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