This package is meant to make it easier for microbiologists to combine and analyse segmentation & fluorescence data derived from custom software like Oufti, Morphometrics, MicrobeJ or Supersegger. There are standard functions for importing several popular programs, but also options for importing CSVs or Matlab files with a specific structure.
BactMAP uses ggplot and many ggplot-extensions to make visual summaries of the segmentation & fluorescence data, show the cell genealogy, plot protein trajectories in the cell and many other things. This can give you a quick overview of your data to make a decision on further analysis and custom visualization.
If you have any comments, requests or find bugs, please report it on the Issues page.
In the wiki you will find a manual and some examples on how to use BactMAP as a gateway between your segmentation & fluorescence data.
#install devtools if not done yet
install.packages("devtools")
#install bactmap from my github repository
devtools::install_github("veeninglab/bactMAP")
#or from the stable build:
devtools::install_github("veeninglab/bactMAP")
#or install it with all dependencies
devtools::install_github("veeninglab/bactMAP", dependencies=TRUE)
#load package
library(bactMAP)
Find the development version here.
This new version contains bug fixes of extr_MicrobeJ and extr_Oufti. It also has a few new functions: orientCells and onePerCell. The first function helps you flip cells based on non-symmetrical fluorescence localization (for instance, a polar fluorescent spot) - the latter is useful if you want to make histograms of cell lengths, etc. based on mesh or object files. A short description of the functions can be found in the manual inside the package (type ?orientCells to find the help of this function, for instance). I will add a small tutorial and documentation to the wiki shortly.