The repository includes the script Source_data_figures.Rmd for reproducing the main figures 1 (B,C,E), 2 (A,D,E,F), 3 (C), 6 (A-I) and the extended figures 1 (A-F), 2 (A-E), 3 (A-G), 4 (A-D), 7 (A-I), 10 (B,C) of the pre-print Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development (https://www.biorxiv.org/content/10.1101/2020.01.15.900613v2).
The input data for running the script is availble in the folder Input_data_figures. Additional three files are needed for the script :
- data_raw.Rda: raw counts matrix for scRNA seq data
- data_tpm.Rda: normalised (TPM) counts matrix for scRNA seq data
- raw_counts_allele_mt.csv: matrix with counts information for the four possible alleles for each base on mitochondrial genome.
Due to their big size, they are not part of this repository.They are available on ArrayExpress (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-8640/) under the section Processed data.