extr_Spots - veeninglab/BactMAP GitHub Wiki

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 cellList=TRUE, the output will contain the dataframe cellList (see below).

Value

A list containing the following dataframes:

  • 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)

Examples

spotpath <- file.choose()

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

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