Code for Morphological profiling of tubercle bacilli identifies drug pathways of action
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Contains two main directories:
## segmentation_pipeline
Inside this directory is the code used to transform the .csv files outputted by MicrobeJ into a MATLAB workspace. This code filters out of focus and blurry cells using the transverse profile and calculates the median, Q1, Q3 and IQR for each replicate.
## classification_and_analysis
Inside this directory is the code used to run the classification trials as outlined in figure S3 as well as code to create the consensus KNN (cKNN) and heatmaps to visualize the results from the classification trials.
In addition, code is included to perform the Kruskal–Wallis tests to determine signfiicance of variables based on using single-cell data and not replicate averages as seen in Figure 1. There is also code to create PCAs that were used in the earlier versions of the analysis pipeline (as seen in Figures 2 and S1).
Performs a classification trial on a workspace created with MicrobeJ_segmentation
Currently set to use default workspaces used in the MophEUS paper, can be adjusted.
Run the script classification_trials.m to run a set of 70 classification trials. Results will be automatically saved into trial_results with the name the user selected along with a timestamp. A log containing all of the output produced during hte run will be saved into the logs folder.
### Before you run
In order to run a classification trial, you need to download Hanchuan Peng's mRMR feature selection algorithm and compile it to work on your operating system. It can be found here:
[mRMR Feature Selection] (https://www.mathworks.com/matlabcentral/fileexchange/14608-mrmr-feature-selection-using-mutual-information-computation?s_tid=prof_contriblnk). Place the resulting mRMR_0.9_compiled folder in the classification_trials directory.