natcommun_hcm_code

natcommun_hcm_code

This R script reproduces part of the figures for the Nat Commun paper (Lai et al., 2021). Should there be any questions or concerns please contact Yunjia directly at yunjia.lai [at] outlook.com.

All rights reserved © Yunjia Lai

Running originally with the following sessionInfo:

R version 4.0.1 (2020-06-06); Platform: X86_64-apple-darwin17.0 (64-bit) or earlier; Running under: macOS 10.16

Matrix products: default; LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

Random number generation: RNG (Mersenne-Twister); Normal (Inversion); Sample (Rounding)

Items

Figure 2a-b & 5a-b. Principal component analysis of fecal ion features

Figure 2e & 5e. Visualization of qMSEA results from Metaboanalyst 4.0

Figure 3a, 6a & 7a. Variable Importance Plots for fecal, serum and brain metabolites

Figure 3c-d, 4a-d & 7b. Box and Whisker plots for assessing group difference

Figure 4g. Heatmap clustering of conjugated fecal metabolites

Figure 8a-b. Analysis of Variance

Figure 8f-h. PieDonut plot for visualizing gender-specificity of metabolites

Code for retention time prediction (adapted from https://www.retip.app/; doi:10.1021/acs.analchem.9b05765)