Creates a figure of a protein's mutational landspace using kernel density estimation.
You might need to install a few packages for the script to work: Biostrings, ggplot2, zoo, and gridExtra.
install.packages(c("ggplot2","zoo","gridExtra"))
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")You can run the script via RStudio after updating the hardcoded arguments, or you can run it from the command line using:
Rscript mutation_kde.R example_data/mutations.txt example_data/aa.txt example_data/domain.txt example_data/P29597.fasta example_data/test.pdfTypically, I would get the FASTA file and domain information from Uniprot.org.
Example output (before manually adjusting label positions):
![Image of example output] (https://github.com/UNC-Major-Lab/KDEMutationPlot/blob/master/example_data/TYK2_KDE.png)
