Bug fixes MicrobeJ import, 2 new functions, better compatibility with curved cells

This version contains a few bug-fixes when it comes to importing data from MicrobeJ and Oufti. Check the wiki and/or documentation for more information on the import functions! It also contains two new functions for analysis after import: orientCells and onePerCell. These functions can be useful to flip cells based on spot or object localization (orientCells) and to summarize data when you're not very familiar with R (onePerCell). Check out the help (by typing ?orientCells or ?onePerCell) to find out how they work.

Bug fixes with importing SuperSegger data

Version 0.1.0.2

In this version, the following improvements are implemented:

1. extr_SuperSeggerCells() import bug in Linux and MacOS fixed.

Version 0.1.0.1

In this version, the following improvements are implemented:

1. Variable name update: Xrotum & Yrotum are now named Xrot_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. We also added a new function checkVersionCompatible() to check your data and solve possible compatibility problems.

2. Installation of ggtree: Now, ggtree is automatically installed upon installation of BactMAP.

3. 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: import functions only give back the dataframe cellList when asked for by setting cellList=TRUE in the function. Other functions where returning of redundant data is turned off are: combineDataframes, createPlotList, Check each individual function documentation for more information.

4. Updated tutorials & example code: Check the BactMAP wiki for updated tutorials, installation instructions & example workflows.