Last updated: 2024-09-19

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Knit directory: madi-project3-sdy8003-pertussis-thailand/

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Serology features PCA - Infant AP vs. WP

vaccinated

Features: DT_ADCD, FHA_ADCD, PRN_ADCD, PT_ADCD, TT_ADCD, DT_ADCP, FHA_ADCP, PRN_ADCP, PT_ADCP, TT_ADCP, DT_ADNP, FHA_ADNP, PRN_ADNP, PT_ADNP, TT_ADNP, DT_FcgR2a, FHA_FcgR2a, PRN_FcgR2a, PT_FcgR2a, TT_FcgR2a, DT_FcgR3b, FHA_FcgR3b, PRN_FcgR3b, PT_FcgR3b, TT_FcgR3b, DT_IgG, FHA_IgG, PRN_IgG, PT_IgG, TT_IgG, DT_IgG1, FHA_IgG1, PRN_IgG1, PT_IgG1, TT_IgG1, DT_IgG2, FHA_IgG2, PRN_IgG2, PT_IgG2, TT_IgG2, DT_IgG3, FHA_IgG3, PRN_IgG3, PT_IgG3, TT_IgG3, DT_IgG4, FHA_IgG4, PRN_IgG4, PT_IgG4, TT_IgG4

Proportion of Variance

Summary for first 5 principal components (PC)
Term PC1 PC2 PC3 PC4 PC5
Standard deviation 3.478 2.500 2.418 1.941 1.888
Proportion of Variance 0.242 0.125 0.117 0.075 0.071
Cumulative Proportion 0.242 0.367 0.484 0.559 0.630

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP vaccinated PC1: p<0.001
Infant AP vs. WP vaccinated PC2: p=0.002

Plot of PCA Eigen Vectors

Correlation between features and each PC score - colored by variance contribution

**Loadings plot

Plot of UMAP1 vs UMAP2 Loadings

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated UMAP1: p<0.001
Infant AP vs. WP vaccinated UMAP2: p<0.001

boosted

Features: DT_ADCD, FHA_ADCD, PRN_ADCD, PT_ADCD, TT_ADCD, DT_ADCP, FHA_ADCP, PRN_ADCP, PT_ADCP, TT_ADCP, DT_ADNP, FHA_ADNP, PRN_ADNP, PT_ADNP, TT_ADNP, DT_FcgR2a, FHA_FcgR2a, PRN_FcgR2a, PT_FcgR2a, TT_FcgR2a, DT_FcgR3b, FHA_FcgR3b, PRN_FcgR3b, PT_FcgR3b, TT_FcgR3b, DT_IgG, FHA_IgG, PRN_IgG, PT_IgG, TT_IgG, DT_IgG1, FHA_IgG1, PRN_IgG1, PT_IgG1, TT_IgG1, DT_IgG2, FHA_IgG2, PRN_IgG2, PT_IgG2, TT_IgG2, DT_IgG3, FHA_IgG3, PRN_IgG3, PT_IgG3, TT_IgG3, DT_IgG4, FHA_IgG4, PRN_IgG4, PT_IgG4, TT_IgG4

Proportion of Variance

Summary for first 5 principal components (PC)
Term PC1 PC2 PC3 PC4 PC5
Standard deviation 3.301 2.583 2.285 1.821 1.699
Proportion of Variance 0.218 0.133 0.104 0.066 0.058
Cumulative Proportion 0.218 0.351 0.456 0.522 0.580

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP boosted PC1: p<0.001
Infant AP vs. WP boosted PC2: p<0.001

Plot of PCA Eigen Vectors

Correlation between features and each PC score - colored by variance contribution

**Loadings plot

Plot of UMAP1 vs UMAP2 Loadings

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted UMAP1: p=0.174
Infant AP vs. WP boosted UMAP2: p<0.001


sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] e1071_1.7-13       glue_1.6.2         mvtnorm_1.2-3      GGally_2.2.1      
 [5] RColorBrewer_1.1-3 scales_1.3.0       umap_0.2.10.0      factoextra_1.0.7  
 [9] gtsummary_1.7.2    gtExtras_0.5.0     gt_0.10.1          broom_1.0.5       
[13] ggpmisc_0.5.5      ggpp_0.5.6         olsrr_0.6.0        cowplot_1.1.1     
[17] ggtext_0.1.2       ggridges_0.5.6     ggfortify_0.4.16   ggpubr_0.6.0      
[21] ggExtra_0.10.1     ggrepel_0.9.3      ggplot2_3.4.4      workflowr_1.7.1   
[25] rmarkdown_2.25     knitr_1.47         gridExtra_2.3      janitor_2.2.0     
[29] data.table_1.14.8  datastepr_0.0.2    stringr_1.5.0      tidyr_1.3.0       
[33] tidyquery_0.2.4    DT_0.28            DBI_1.1.3          RPostgres_1.4.5   
[37] dplyr_1.1.2        here_1.0.1        

loaded via a namespace (and not attached):
 [1] rstudioapi_0.15.0    jsonlite_1.8.7       magrittr_2.0.3      
 [4] farver_2.1.1         fs_1.6.3             vctrs_0.6.3         
 [7] paletteer_1.6.0      askpass_1.2.0        rstatix_0.7.2       
[10] htmltools_0.5.8      polynom_1.4-1        sass_0.4.9          
[13] bslib_0.7.0          htmlwidgets_1.6.2    fontawesome_0.5.2   
[16] plyr_1.8.9           lubridate_1.9.2      cachem_1.0.8        
[19] whisker_0.4.1        mime_0.12            lifecycle_1.0.4     
[22] pkgconfig_2.0.3      Matrix_1.6-1.1       R6_2.5.1            
[25] fastmap_1.1.1        shiny_1.7.4.1        snakecase_0.11.1    
[28] digest_0.6.33        colorspace_2.1-0     rematch2_2.1.2      
[31] ps_1.7.5             rprojroot_2.0.4      RSpectra_0.16-1     
[34] labeling_0.4.3       fansi_1.0.4          timechange_0.2.0    
[37] httr_1.4.7           abind_1.4-5          compiler_4.3.1      
[40] proxy_0.4-27         bit64_4.0.5          withr_3.0.0         
[43] backports_1.4.1      carData_3.0-5        ggstats_0.5.1       
[46] highr_0.11           ggsignif_0.6.4       MASS_7.3-60.0.1     
[49] quantreg_5.97        openssl_2.1.1        tools_4.3.1         
[52] httpuv_1.6.11        goftest_1.2-3        callr_3.7.5         
[55] promises_1.2.0.1     gridtext_0.1.5       getPass_0.2-2       
[58] generics_0.1.3       gtable_0.3.4         nortest_1.0-4       
[61] class_7.3-22         hms_1.1.3            xml2_1.3.5          
[64] car_3.1-2            utf8_1.2.3           pillar_1.9.0        
[67] later_1.3.1          splines_4.3.1        queryparser_0.3.2   
[70] lattice_0.21-8       survival_3.5-5       bit_4.0.5           
[73] SparseM_1.81         tidyselect_1.2.0     miniUI_0.1.1.1      
[76] git2r_0.32.0         xfun_0.45            stringi_1.7.12      
[79] lazyeval_0.2.2       yaml_2.3.7           evaluate_0.23       
[82] tibble_3.2.1         cli_3.6.1            xtable_1.8-4        
[85] reticulate_1.37.0    munsell_0.5.0        processx_3.8.2      
[88] jquerylib_0.1.4      Rcpp_1.0.11          png_0.1-8           
[91] MatrixModels_0.5-3   ellipsis_0.3.2       blob_1.2.4          
[94] broom.helpers_1.14.0 purrr_1.0.1          rlang_1.1.1