Scripts used for generating figures of the DGRPool manuscript
Vincent Gardeux, Roel PJ Bevers, Fabrice PA David, Emily Rosschaert, Romain Rochepeau and Bart Deplancke, (2024) DGRPool: A web tool leveraging harmonized Drosophila Genetic Reference Panel phenotyping data for the study of complex traits, eLife, 12:RP88981 https://doi.org/10.7554/eLife.88981.3
In order to be fully reproducible, we downloaded the phenotypes on the website at a given timepoint. The script used, 1_download_phenotypes.R, access our API to download a "studies.json" file containing all metadata for each study. Then it uses the same API to download the phenotypes study by study, and format everything in a common format. It then generates a RDS file with a given timestamp, which is the common file used by all other methods, so that all scripts are using the same data, collected at a given timestamp. We here provided the data used in the latest version of the manuscript in data.all_pheno_15_07_24_filtered.rds, but you can run again 1_download_phenotypes.R to generate a new RDS with the latest up-to-date phenotyping data.
We also created a script, 2_correlation_phenotypes.R, to generate all correlations across phenotypes. This is generating correlation files in the resources folder, which are then used by other scripts (such as Figure 2A, 2B, S5).
All scripts needed to reproduce Figures of the paper are in their respective FigureXX folders. In general they are all using the timestamped RDS file that is present in the RDS folder (see Reproducibility section).
In the GWAS folder, we provide the two R scripts that are used to generate the GWAS results. Both for the pre-calculated GWAS ran for all phenotypes in the DGRPool database (running_GWAS.R), and for the user-submitted GWAS (running_GWAS_user.R). It requires PLINK2 to be installed on the machine to run correctly. Variant annotation and covariate files are also in the GWAS folder.
Since it can be hard to find DGRP/bloomington mapping files, especially for old DGRP lines, we provide a mapping file here: resources/DGRP_Bloomington_Mapping.txt