A number of functions are needed for genomic plotting and can be found here as well as here
The analysis for the ds genomic artificial selection, including the plotting of Fst and GO analyses can be found in this script. There is also a related analysis for emc
This analysis creates supplemental figure 22 and this associated script for supplemental figure 25.
CMH test for pooled data was done using the ACER package. All scripts for this are indicated with ACER in the title but a representative can be found here.
This script will recreate the correlation plot between shape change vectors and DGRP PCs.
This script contains analysis for wild populations, including correlation with shape change vectors and phenotypic variation between populations.
This analysis describes the analysis of the response to selection from ds shape change. There is also a related analysis for emc change change selection.
First, the sync file needed to be converted into reference and alternate allele counts using this
Then genetic distances could be compared with phenotypic distances (calculated in this analysis) using vegan see here
this script creates supplemental figure 1
this combines multiple analyses into single figures.
this script creates supplemental figure 5