extr_Spots: Generic function for extraction of spot data

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

Generic function for extraction of spot data

Description

To upload spot localization data to R in the standard BactMAP format, save your spot data as a .txt or .csv file with (at least) the following columns:

x - the x coordinate of each spot

y - the y coordinate of each spot

frame - the number of the image frame

The function also recognises the following columns:

trajectory - ID variable for a spot trajectory

trajectory_length - the recorded length of each trajectory

displacement_sq - the squared displacement of each spot

Other columns will be saved in the output "cellList" (see below).

Usage

extr_Spots(dataloc, seperator = ",", cellList=FALSE)

Arguments

dataloc	The path to the .txt or .csv file containing the spot data.
seperator	Indicates the column seperator of the .txt or .csv. Default = ","
cellList	When TRUE, the value 'cellList' is returned (see below).

Value

cellList	the original input data as dataframe
spotframe	dataframe containing the minimal required columns (x, y & frame) and if given, the extra columns (trajectory, trajectory_length & displacement_sq)

Author(s)

Renske van Raaphorst

Examples

## Not run: 
spotpath <- file.choose()

spot_output <- extr_Spots(spotpath, seperator="/t")$spotframe

## End(Not run)

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