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!! 06.2020 - If you have problems with your installed R packages since the update to R4.0.0, check out the installation page
!! 31.03.2020 One user found an error in BactMAP today now causing trouble with plotting heatmaps of spots in cells. I resolved this problem and saved this in the development version of BactMAP. The following days I will check it and implement an update. In the meantime: please download BactMAP from the development page using:
remotes::install_github("vrrenske/bactmap")
This package is made to make it easier for microbiologists to combine and analyse segmentation & fluorescence data derived from custom softwares like Oufti, Morphometrics, MicrobeJ or Supersegger. There are standard functions for importing several popular programs, but also options for importing CSVs with a specific structure. If your favorite segmentation or spot detection program is missing, let me know by opening an issue/request on this page.
BactMAP uses ggplot to make visual summaries of the segmentation & fluorescence data, show the cell genealogy, plot protein trajectories in the cell and many other things. This will give you a quick overview of your data to make a decision on further analysis and custom visualization.
This Wiki contains a manual, function documentation and examples on how to use BactMAP. Navigate through the side bar to get started.
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Variable name update:
Xrotum&Yrotumare now namedXrot_micron&Yrot_micron. Functions using these variables have been updated and should recognize both the old and the new variable names. In case something doesn't work with old datasets, please contact us via email or post an issue on this page. We also added a new functioncheckVersionCompatibleto check your data and solve possible compatibility problems. -
Installation of
ggtree: Now,ggtreeis automatically installed upon installation of BactMAP. If you still encounter installation problems, check possible solutions here and here (Mac). -
Leaner functions: Import functions & plotting functions are now set to return only the most commonly used datasets, unless asked for more, to keep more working memory free. In practice, this means that:
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import functions only give back the dataframe
cellListwhen asked for by settingcellList=TRUEin the function. -
Other functions where returning of redundant data is turned off are:
combineDataframes,createPlotListandspotsInBox. -
Check each individual function documentation for more information.
- Updated tutorials & example code: Browse through the Side Bar for updated tutorials, installation instructions & example workflows.
van Raaphorst, R., Kjos, M., & Veening, J. W. (2020). BactMAP: An R package for integrating, analyzing and visualizing bacterial microscopy data. Molecular microbiology, 113(1), 297-308.
