This is the repository belonging to the paper "The impact of the cardiovascular component and somatic mutation on ageing" by Garger et al.
The "Supplementary Table 1.xlsx" - "1j - Data for analysis" sheet contains the data which is used for the analysis.
- The CreateFigure.R file contains the code for executing the analysis of the paper. Furthermore, figures 2 & 3 and supplementary table 4 can be reproduced.
- Create_Figure_1_and_Supplementary_Figs.Rmd file creates the phylogenetic tree used for phylogenetic analysis, also creates a basic version of Figure 1 (final version created with Adobe Illustrator), and also all Supplementary Figures along with required analysis (phylogenetic regression, bootstrapping analysis).
We used R 4.1.2 and the following libraries for the analysis:
- readxl
- ggplot2
- tidyverse
- ggrepel
- reshape2
- broom
- ppcor
- scatterplot3d
- factoextra
- FactoMineR
- PCAtools
- boot
- ape
- ade4
- dplyr
- caper
- nlme
- gridExtra
- phytools
- colorspace
- ggpubr
- lemon
- gplots
- devtools
- ggtree
- cowplot
- colorspace
- ggplotify
- ComplexHeatmap
- writexl