View source: R/Extr_Morphometrics.R
extr_Morphometrics | R Documentation |
The 'CONTOURS'-output from Morphometrics is uploaded and converted to a *mesh*-dataframe compatible with bactMAPs plotting functions. Find more examples of usage of extr_Morphometrics
on the BactMAP wiki.
extr_Morphometrics(morphpath, mag, turncells = TRUE, cellList=FALSE)
morphpath |
the path to the 'CONTOURS'- output of Morphometrics (for instance "mycells_01-01-2019_CONTOURS.mat"). |
mag |
pixel conversion factor (see pixels2um). if added, the coordinates and cell length/width will be converted to micron |
turncells |
if set to TRUE (default), X and Y coordinates will be turned so that mid-cell is at [0,0], while the length axis of the cell's bounding box is parallel to the x axis. |
cellList |
when cellList==TRUE, the value |
cellList |
dataframe containing the original data extracted from Morphometrics. |
mesh |
dataframe containing the coordinates of the outlines of the cell, cell dimensions and if *turncells==TRUE*, the coordinates of each cell turned and repositioned to [0,0] |
pixel2um |
if *mag* was defined in the arguments, the conversion factor is saved in the output list. |
Renske van Raaphorst
Ursell T, Lee TK, Shiomi D, et al. Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library. BMC Biol. 2017;15(1):17. Published 2017 Feb 21. doi:10.1186/s12915-017-0348-8
## Not run:
#Upload Morphometrics output from bactMAP example files
Example_MM <- file.choose()
Example_output <- extr_Morphometrics(Example_MM)$mesh
#check output:
summary(Example_output)
#plot cells
plotRaw(Example_output, frameN=1)
## End(Not run)
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