object: Object DataFrames

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

Object DataFrames

Description

A dataframe containing object information, either objectframe or object_relative.

These dataframes can be used in various of the bactMAP functions: plotTracks, plotObjects, plotOverlay & plotRaw.

Format

In the case of objectframe, the most basic of the two, the object coordinates and cell information are given:

ob_x

the x-coordinate (in pixels) of the object shape outline

ob_y

the y-coordinate (in pixels) of the object shape outline

obnum

the number of the object inside one cell

obpath

number indicates the order of the object coordinates, so a polygon will be drawn correctly

frame

the number of the image frame

cell

the number of the bacterial cell

obID

unique object identifier

In the case of object_relative, the following colums are added:

max.length

the cell length of the given cell the object is in.

num

a rank for the cell size - the smaller num, the smaller the cell size

max.width

the cell width of the given cell this object is in.

Dum

the relative localization of the mid-point of the object on the width axis of the cell, in micron.

Lmid

the relative localization of the mid-point of the object on the length axis of the cell, in micron.

ob_out_x

the relative x-coordinate (in micron) of the object shape outline to the cell

ob_out_y

the relative y-coordinate (in micron) of the object shape outline to the cell

pole1

the distance of one cell pole to mid-cell

pole2

the distance of the other cell pole to mid-cell. Since mid-cell is placed at [0,0], this is always the negative of pole1.

max_um

max.length in micron

maxwum

max.width in micron

Details

An example of an object dataframe can be taken from the bactMAP package. How is shown in "examples" below.

Examples

## Not run: 
#take VanFL object data from https://veeninglab.com/f/example_datasets.zip
load("VanFL_objWT.rda")

summary(VanFL_objWT.rda)


## End(Not run)

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