RMS Analysis

The scripts contained here cover the analyses for:

Fullmer, M.S., Ouellette, M., Louyakis, A.S., Papke, R.T., and Gogarten, J.P., (in review). The patchy distribution of restriction-modification system genes and the conservation of orphan methyltransferases in halobacteria. Gene

rms.RMD:

R scripts for heatmap with tree, interactive heatmap, genomes per cHG barplot, rarefaction plot, and correlation plot

input_files:

Contains the input files used to make the figures

cHGperGenome.txt
ConcatAlnRooted.tre
PresAbsMatrixAnnot.txt
PresAbsSummary.txt
reorder.txt
uniprot_arcog.txt

output_files

Contains the raw output for the figures listed in the paper

cHGperGenome.pdf
corrplot.pdf
heatmaply_plot.html (with directory of files)
heattree.pdf
rarefaction_plot.pdf

code for input_files