This repository converts an analysis of MAP data using broad human anti-HIV sera and HIV Envelope strain BG505, performed and written by Adam Dingens, into interactive plots. This repository was made by Caelan Radford.
The adingens_analysis folder contains the analysis written by Adam Dingens. Caelan did not modify its contents. This folder contains its own documentation, which should be viewed for details on that analysis.
The calculate_fraction_surviving_all_sera.ipynb calculates the fraction surviving statistic for each serum selection, which were not calculated previously. The results folder contains the results from these calculations.
The generate_interactive_plots.ipynb converts the results from Adam Dingens' analysis into interactive plots from the polyclonal software. Because these plots are produced outside of a pipeline like the dms-vep-pipeline, they will not contain as much information as plots produced by that pipeline, such as this one.
The interactive_plots folder contains the interactive plots produced in html files.
The results_from_lentivirus_dms folder contains interactive plots produced from lentivirus deep mutational scanning using the BF520 strain for some of these same sera. You can view the pre-print describing this work here.
The analysis in the adingens_analysis folder and the generate_interactive_plots.ipynb need a computing environment that contains dms_tools2. A compatible conda environment can be found here.
The conversion performed in generate_interactive_plots.ipynb can use the environment dms-vep-pipeline, found here.