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