Last updated: 2024-11-25

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File Version Author Date Message
Rmd 4461231 alecbuetow 2024-11-25 corrected mislabeled file name
Rmd 5dae9d3 alecbuetow 2024-11-25 added supervised clusters
Rmd c432a7f Michael S. Zens 2024-09-16 added feature_comparisions and fixed the deimension reduction for 6 variations of clustering for each manuscript.
Rmd 688280f Michael S. Zens 2024-04-24 expanded set of ap-wp analyses following David and Lisa
html 688280f Michael S. Zens 2024-04-24 expanded set of ap-wp analyses following David and Lisa

Infant AP vs. WP visit:vaccinated - vaccinated : PCA Results

Antigen: PT

Features: PT_ADCD, PT_ADCP, PT_ADNP, PT_FcgR2a, PT_FcgR3b, PT_IgG1, PT_IgG3, PT_IgG2, PT_IgG4, PT_IgG

Proportion of Variance

Summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.983 1.309 1.071 0.835 0.796
Proportion of Variance 0.393 0.171 0.115 0.070 0.063
Cumulative Proportion 0.393 0.565 0.679 0.749 0.812

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated PT PC1: p=.13
Infant AP vs. WP vaccinated PT PC2: p<.0001

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated PT UMAP1: p=.00022
Infant AP vs. WP vaccinated PT UMAP2: p<.0001

Antigen: FHA

Features: FHA_ADCD, FHA_ADCP, FHA_ADNP, FHA_IgG3, FHA_IgG1, FHA_IgG2, FHA_IgG4, FHA_FcgR2a, FHA_FcgR3b, FHA_IgG

Proportion of Variance

Summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.839 1.322 1.169 0.993 0.843
Proportion of Variance 0.338 0.175 0.137 0.099 0.071
Cumulative Proportion 0.338 0.513 0.649 0.748 0.819

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated FHA PC1: p=.34
Infant AP vs. WP vaccinated FHA PC2: p<.0001

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated FHA UMAP1: p<.0001
Infant AP vs. WP vaccinated FHA UMAP2: p<.0001

Antigen: PRN

Features: PRN_ADCD, PRN_ADNP, PRN_ADCP, PRN_IgG3, PRN_IgG1, PRN_IgG2, PRN_IgG4, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG

Proportion of Variance

Summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.634 1.294 1.060 1.054 0.930
Proportion of Variance 0.267 0.168 0.112 0.111 0.087
Cumulative Proportion 0.267 0.434 0.547 0.658 0.744

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated PRN PC1: p=.21
Infant AP vs. WP vaccinated PRN PC2: p<.0001

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated PRN UMAP1: p=.84
Infant AP vs. WP vaccinated PRN UMAP2: p<.0001

Antigen: DT

Features: DT_ADCD, DT_ADCP, DT_ADNP, DT_FcgR2a, DT_FcgR3b, DT_IgG3, DT_IgG1, DT_IgG2, DT_IgG4, DT_IgG

Proportion of Variance

Summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.640 1.334 1.231 1.067 0.963
Proportion of Variance 0.269 0.178 0.152 0.114 0.093
Cumulative Proportion 0.269 0.447 0.599 0.712 0.805

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated DT PC1: p=.15
Infant AP vs. WP vaccinated DT PC2: p<.0001

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated DT UMAP1: p<.0001
Infant AP vs. WP vaccinated DT UMAP2: p<.0001

Antigen: TT

Features: TT_ADCD, TT_FcgR2a, TT_IgG3, TT_IgG1, TT_IgG2, TT_IgG4, TT_ADCP, TT_ADNP, TT_FcgR3b, TT_IgG

Proportion of Variance

Summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.986 1.290 0.969 0.957 0.866
Proportion of Variance 0.395 0.166 0.094 0.092 0.075
Cumulative Proportion 0.395 0.561 0.655 0.747 0.822

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated TT PC1: p=.041
Infant AP vs. WP vaccinated TT PC2: p<.0001

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p<.0001
Infant AP vs. WP vaccinated TT UMAP2: p=.041

Feature Cluster: IgG2 / IgG4

Features: DT_IgG2, DT_IgG4, FHA_IgG2, FHA_IgG4, PRN_IgG2, PRN_IgG4, PT_IgG2, PT_IgG4, TT_IgG2, TT_IgG4

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10
Standard deviation 2.291 1.016 0.961 0.868 0.724 0.677 0.602 0.545 0.453 0.441
Proportion of Variance 0.525 0.103 0.092 0.075 0.052 0.046 0.036 0.030 0.021 0.019
Cumulative Proportion 0.525 0.628 0.721 0.796 0.848 0.894 0.930 0.960 0.981 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster IgG2 / IgG4 PC1: p<.0001
Infant AP vs. WP vaccinated Feature Cluster IgG2 / IgG4 PC2: p=.063

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.0021
Infant AP vs. WP vaccinated TT UMAP2: p<.0001

Feature Cluster: ADCD

Features: DT_ADCD, FHA_ADCD, PRN_ADCD, TT_ADCD, PT_ADCD

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.858 0.810 0.738 0.471 0.356
Proportion of Variance 0.690 0.131 0.109 0.044 0.025
Cumulative Proportion 0.690 0.821 0.930 0.975 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster ADCD PC1: p=.77
Infant AP vs. WP vaccinated Feature Cluster ADCD PC2: p=.37

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.17
Infant AP vs. WP vaccinated TT UMAP2: p=.87

Feature Cluster: ADNP / ADCP

Features: DT_ADCP, PRN_ADNP, DT_ADNP, FHA_ADCP, FHA_ADNP, PRN_ADCP, PT_ADCP, PT_ADNP, TT_ADCP, TT_ADNP

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10
Standard deviation 1.691 1.371 1.093 1.027 0.864 0.765 0.753 0.708 0.567 0.542
Proportion of Variance 0.286 0.188 0.119 0.105 0.075 0.058 0.057 0.050 0.032 0.029
Cumulative Proportion 0.286 0.474 0.593 0.699 0.773 0.832 0.888 0.938 0.971 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster ADNP / ADCP PC1: p=.007
Infant AP vs. WP vaccinated Feature Cluster ADNP / ADCP PC2: p=.72

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.0041
Infant AP vs. WP vaccinated TT UMAP2: p=.43

Feature Cluster: FcgR2a / FcgR3b

Features: DT_FcgR2a, DT_FcgR3b, PT_FcgR2a, PT_FcgR3b, TT_FcgR2a, FHA_FcgR2a, FHA_FcgR3b, PRN_FcgR2a, PRN_FcgR3b, TT_FcgR3b

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10
Standard deviation 2.483 1.134 0.865 0.786 0.680 0.580 0.406 0.306 0.268 0.229
Proportion of Variance 0.617 0.128 0.075 0.062 0.046 0.034 0.016 0.009 0.007 0.005
Cumulative Proportion 0.617 0.745 0.820 0.882 0.928 0.962 0.978 0.988 0.995 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster FcgR2a / FcgR3b PC1: p=.85
Infant AP vs. WP vaccinated Feature Cluster FcgR2a / FcgR3b PC2: p=.79

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.9
Infant AP vs. WP vaccinated TT UMAP2: p=.22

Feature Cluster: IgG1

Features: PT_IgG1, DT_IgG1, FHA_IgG1, PRN_IgG1, TT_IgG1

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.696 0.907 0.782 0.673 0.488
Proportion of Variance 0.575 0.165 0.122 0.091 0.048
Cumulative Proportion 0.575 0.740 0.862 0.952 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster IgG1 PC1: p=.73
Infant AP vs. WP vaccinated Feature Cluster IgG1 PC2: p=.87

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.95
Infant AP vs. WP vaccinated TT UMAP2: p=.59

Feature Cluster: IgG3

Features: DT_IgG3, FHA_IgG3, PRN_IgG3, PT_IgG3, TT_IgG3

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.735 0.808 0.755 0.624 0.613
Proportion of Variance 0.602 0.131 0.114 0.078 0.075
Cumulative Proportion 0.602 0.733 0.847 0.925 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster IgG3 PC1: p=.28
Infant AP vs. WP vaccinated Feature Cluster IgG3 PC2: p=.28

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.34
Infant AP vs. WP vaccinated TT UMAP2: p=.19

Feature Cluster: IgG

Features: DT_IgG, FHA_IgG, PRN_IgG, PT_IgG, TT_IgG

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.666 0.929 0.822 0.657 0.505
Proportion of Variance 0.555 0.173 0.135 0.086 0.051
Cumulative Proportion 0.555 0.728 0.863 0.949 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster IgG PC1: p=.00038
Infant AP vs. WP vaccinated Feature Cluster IgG PC2: p=.18

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.42
Infant AP vs. WP vaccinated TT UMAP2: p<.0001

Response Cluster: 1

Features: DT_ADCD, DT_ADCP, FHA_ADCD, PRN_ADCD, PRN_ADNP, TT_ADCD, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6
Standard deviation 1.764 1.016 0.972 0.730 0.505 0.354
Proportion of Variance 0.518 0.172 0.158 0.089 0.042 0.021
Cumulative Proportion 0.518 0.690 0.848 0.937 0.979 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 1 PC1: p=.98
Infant AP vs. WP vaccinated RCluster_ 1 PC2: p=.65

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.94
Infant AP vs. WP vaccinated TT UMAP2: p=.76

Response Cluster: 2

Features: DT_ADNP, FHA_ADCP, FHA_ADNP, PRN_ADCP, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4
Standard deviation 1.435 0.917 0.790 0.690
Proportion of Variance 0.514 0.210 0.156 0.119
Cumulative Proportion 0.514 0.725 0.881 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 2 PC1: p=.031
Infant AP vs. WP vaccinated RCluster_ 2 PC2: p=.6

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.8
Infant AP vs. WP vaccinated TT UMAP2: p=.13

Response Cluster: 3

Features: DT_FcgR2a, DT_FcgR3b, DT_IgG3, FHA_IgG3, PRN_IgG3, PT_ADCD, PT_ADCP, PT_ADNP, PT_FcgR2a, PT_FcgR3b, PT_IgG1, PT_IgG3, TT_FcgR2a, TT_IgG3, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 PC14
Standard deviation 2.474 1.454 0.994 0.943 0.828 0.818 0.755 0.695 0.684 0.602 0.540 0.486 0.263 0.230
Proportion of Variance 0.437 0.151 0.070 0.064 0.049 0.048 0.041 0.035 0.033 0.026 0.021 0.017 0.005 0.004
Cumulative Proportion 0.437 0.588 0.659 0.722 0.771 0.819 0.860 0.894 0.928 0.954 0.974 0.991 0.996 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 3 PC1: p=.39
Infant AP vs. WP vaccinated RCluster_ 3 PC2: p=.52

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.077
Infant AP vs. WP vaccinated TT UMAP2: p=.5

Response Cluster: 4

Features: DT_IgG1, FHA_IgG1, PRN_IgG1, TT_IgG1, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4
Standard deviation 1.589 0.818 0.729 0.526
Proportion of Variance 0.631 0.167 0.133 0.069
Cumulative Proportion 0.631 0.798 0.931 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 4 PC1: p=.81
Infant AP vs. WP vaccinated RCluster_ 4 PC2: p=.021

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.7
Infant AP vs. WP vaccinated TT UMAP2: p=.12

Response Cluster: 5

Features: DT_IgG2, DT_IgG4, FHA_IgG2, FHA_IgG4, PRN_IgG2, PRN_IgG4, PT_IgG2, PT_IgG4, TT_IgG2, TT_IgG4, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10
Standard deviation 2.291 1.016 0.961 0.868 0.724 0.677 0.602 0.545 0.453 0.441
Proportion of Variance 0.525 0.103 0.092 0.075 0.052 0.046 0.036 0.030 0.021 0.019
Cumulative Proportion 0.525 0.628 0.721 0.796 0.848 0.894 0.930 0.960 0.981 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 5 PC1: p<.0001
Infant AP vs. WP vaccinated RCluster_ 5 PC2: p=.063

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.0021
Infant AP vs. WP vaccinated TT UMAP2: p<.0001

Response Cluster: 6

Features: FHA_FcgR2a, FHA_FcgR3b, PRN_FcgR2a, PRN_FcgR3b, TT_ADCP, TT_ADNP, TT_FcgR3b, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7
Standard deviation 2.055 1.004 0.841 0.657 0.562 0.459 0.324
Proportion of Variance 0.603 0.144 0.101 0.062 0.045 0.030 0.015
Cumulative Proportion 0.603 0.747 0.848 0.910 0.955 0.985 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 6 PC1: p=.31
Infant AP vs. WP vaccinated RCluster_ 6 PC2: p=.0031

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.83
Infant AP vs. WP vaccinated TT UMAP2: p=.024

Response Cluster: NA

Features: NA

Infant AP vs. WP visit: boosted - boosted : PCA Results

Antigen: PT

Features: PT_ADCD, PT_IgG1, PT_ADNP, PT_IgG3, PT_IgG2, PT_IgG4, PT_ADCP, PT_FcgR2a, PT_FcgR3b, PT_IgG

Proportion of Variance

Summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.822 1.361 1.106 0.930 0.886
Proportion of Variance 0.332 0.185 0.122 0.086 0.078
Cumulative Proportion 0.332 0.517 0.639 0.726 0.804

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP boosted PT PC1: p=.00043
Infant AP vs. WP boosted PT PC2: p<.0001

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted PT UMAP1: p<.0001
Infant AP vs. WP boosted PT UMAP2: p<.0001

Antigen: FHA

Features: FHA_ADCD, FHA_IgG1, FHA_IgG2, FHA_IgG4, FHA_ADCP, FHA_IgG3, FHA_ADNP, FHA_FcgR2a, FHA_FcgR3b, FHA_IgG

Proportion of Variance

Summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.882 1.186 1.130 0.972 0.903
Proportion of Variance 0.354 0.141 0.128 0.095 0.082
Cumulative Proportion 0.354 0.495 0.623 0.717 0.799

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP boosted FHA PC1: p=.00087
Infant AP vs. WP boosted FHA PC2: p<.0001

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted FHA UMAP1: p=.0052
Infant AP vs. WP boosted FHA UMAP2: p<.0001

Antigen: PRN

Features: PRN_ADCD, PRN_IgG1, PRN_ADNP, PRN_IgG2, PRN_IgG4, PRN_ADCP, PRN_IgG3, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG

Proportion of Variance

Summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.589 1.386 1.118 1.033 1.007
Proportion of Variance 0.252 0.192 0.125 0.107 0.101
Cumulative Proportion 0.252 0.444 0.569 0.676 0.778

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP boosted PRN PC1: p=.27
Infant AP vs. WP boosted PRN PC2: p<.0001

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted PRN UMAP1: p=.05
Infant AP vs. WP boosted PRN UMAP2: p<.0001

Antigen: DT

Features: DT_ADCD, DT_ADCP, DT_ADNP, DT_IgG1, DT_FcgR2a, DT_FcgR3b, DT_IgG4, DT_IgG2, DT_IgG3, DT_IgG

Proportion of Variance

Summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.442 1.288 1.207 1.161 1.070
Proportion of Variance 0.208 0.166 0.146 0.135 0.114
Cumulative Proportion 0.208 0.374 0.520 0.655 0.769

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP boosted DT PC1: p=.55
Infant AP vs. WP boosted DT PC2: p=.0057

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted DT UMAP1: p=.00072
Infant AP vs. WP boosted DT UMAP2: p=.024

Antigen: TT

Features: TT_ADCD, TT_FcgR2a, TT_IgG1, TT_ADNP, TT_IgG2, TT_IgG4, TT_ADCP, TT_IgG3, TT_FcgR3b, TT_IgG

Proportion of Variance

Summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.716 1.187 1.130 1.056 0.940
Proportion of Variance 0.294 0.141 0.128 0.112 0.088
Cumulative Proportion 0.294 0.435 0.563 0.675 0.763

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP boosted TT PC1: p<.0001
Infant AP vs. WP boosted TT PC2: p=.006

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p<.0001
Infant AP vs. WP boosted TT UMAP2: p<.0001

Feature Cluster: IgG2 / IgG4

Features: DT_IgG4, DT_IgG2, FHA_IgG2, FHA_IgG4, PRN_IgG2, PRN_IgG4, PT_IgG2, PT_IgG4, TT_IgG2, TT_IgG4

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10
Standard deviation 2.350 0.979 0.967 0.847 0.781 0.715 0.558 0.405 0.395 0.336
Proportion of Variance 0.552 0.096 0.093 0.072 0.061 0.051 0.031 0.016 0.016 0.011
Cumulative Proportion 0.552 0.648 0.742 0.813 0.874 0.926 0.957 0.973 0.989 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster IgG2 / IgG4 PC1: p<.0001
Infant AP vs. WP boosted Feature Cluster IgG2 / IgG4 PC2: p=.53

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p<.0001
Infant AP vs. WP boosted TT UMAP2: p<.0001

Feature Cluster: ADCD

Features: DT_ADCD, FHA_ADCD, PRN_ADCD, PT_ADCD, TT_ADCD

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.899 0.728 0.602 0.558 0.433
Proportion of Variance 0.722 0.106 0.073 0.062 0.038
Cumulative Proportion 0.722 0.828 0.900 0.962 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster ADCD PC1: p=.99
Infant AP vs. WP boosted Feature Cluster ADCD PC2: p=.0018

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.94
Infant AP vs. WP boosted TT UMAP2: p=.83

Feature Cluster: ADNP / ADCP

Features: DT_ADCP, DT_ADNP, PRN_ADNP, PT_ADNP, TT_ADNP, FHA_ADCP, PRN_ADCP, TT_ADCP, FHA_ADNP, PT_ADCP

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10
Standard deviation 1.717 1.404 1.195 0.963 0.851 0.780 0.705 0.625 0.544 0.458
Proportion of Variance 0.295 0.197 0.143 0.093 0.072 0.061 0.050 0.039 0.030 0.021
Cumulative Proportion 0.295 0.492 0.635 0.728 0.800 0.861 0.910 0.949 0.979 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster ADNP / ADCP PC1: p=.14
Infant AP vs. WP boosted Feature Cluster ADNP / ADCP PC2: p=.099

Plot of PCA Eigen Vectors

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

Version Author Date
688280f Michael S. Zens 2024-04-24

**Loadings plot

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of UMAP1 vs UMAP2 Loadings

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.82
Infant AP vs. WP boosted TT UMAP2: p=.47

Feature Cluster: FcgR2a / FcgR3b

Features: TT_FcgR2a, DT_FcgR2a, DT_FcgR3b, FHA_FcgR2a, FHA_FcgR3b, PRN_FcgR2a, PRN_FcgR3b, PT_FcgR2a, PT_FcgR3b, TT_FcgR3b

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10
Standard deviation 2.136 1.283 1.087 0.966 0.843 0.716 0.436 0.373 0.290 0.197
Proportion of Variance 0.456 0.165 0.118 0.093 0.071 0.051 0.019 0.014 0.008 0.004
Cumulative Proportion 0.456 0.621 0.739 0.832 0.904 0.955 0.974 0.988 0.996 1.000

Version Author Date
688280f Michael S. Zens 2024-04-24

Plot of PC1 vs PC2 scores

Version Author Date
688280f Michael S. Zens 2024-04-24

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster FcgR2a / FcgR3b PC1: p=.41
Infant AP vs. WP boosted Feature Cluster FcgR2a / FcgR3b PC2: p=.0046

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 TT UMAP1: p=.35
Infant AP vs. WP boosted TT UMAP2: p=.027

Feature Cluster: IgG1

Features: DT_IgG1, FHA_IgG1, PRN_IgG1, PT_IgG1, TT_IgG1

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.669 0.862 0.747 0.705 0.646
Proportion of Variance 0.557 0.149 0.112 0.099 0.084
Cumulative Proportion 0.557 0.706 0.817 0.916 1.000

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster IgG1 PC1: p=.71
Infant AP vs. WP boosted Feature Cluster IgG1 PC2: p=.61

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 TT UMAP1: p=.58
Infant AP vs. WP boosted TT UMAP2: p=.48

Feature Cluster: IgG3

Features: PT_IgG3, DT_IgG3, FHA_IgG3, PRN_IgG3, TT_IgG3

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.533 0.945 0.814 0.764 0.714
Proportion of Variance 0.470 0.178 0.133 0.117 0.102
Cumulative Proportion 0.470 0.649 0.781 0.898 1.000

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster IgG3 PC1: p=.21
Infant AP vs. WP boosted Feature Cluster IgG3 PC2: p=1

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 TT UMAP1: p=.65
Infant AP vs. WP boosted TT UMAP2: p=.26

Feature Cluster: IgG

Features: DT_IgG, FHA_IgG, PRN_IgG, PT_IgG, TT_IgG

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5
Standard deviation 1.825 0.784 0.736 0.568 0.437
Proportion of Variance 0.666 0.123 0.108 0.065 0.038
Cumulative Proportion 0.666 0.789 0.897 0.962 1.000

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster IgG PC1: p=.069
Infant AP vs. WP boosted Feature Cluster IgG PC2: p=.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 boosted TT UMAP1: p=.21
Infant AP vs. WP boosted TT UMAP2: p=.00028

Response Cluster: 1

Features: DT_ADCD, FHA_ADCD, PRN_ADCD, PT_ADCD, TT_ADCD, TT_FcgR2a, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6
Standard deviation 1.973 0.879 0.720 0.598 0.539 0.410
Proportion of Variance 0.649 0.129 0.086 0.060 0.048 0.028
Cumulative Proportion 0.649 0.778 0.864 0.924 0.972 1.000

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 1 PC1: p=.84
Infant AP vs. WP boosted RCluster_ 1 PC2: p=.26

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 TT UMAP1: p=.4
Infant AP vs. WP boosted TT UMAP2: p=.82

Response Cluster: 2

Features: DT_ADCP, DT_ADNP, DT_IgG1, FHA_IgG1, PRN_IgG1, PT_IgG1, TT_IgG1, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7
Standard deviation 1.702 1.152 0.884 0.785 0.730 0.677 0.624
Proportion of Variance 0.414 0.189 0.112 0.088 0.076 0.065 0.056
Cumulative Proportion 0.414 0.603 0.715 0.803 0.879 0.944 1.000

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 2 PC1: p=.52
Infant AP vs. WP boosted RCluster_ 2 PC2: p=.11

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 TT UMAP1: p=.53
Infant AP vs. WP boosted TT UMAP2: p=.97

Response Cluster: 3

Features: DT_FcgR2a, DT_FcgR3b, DT_IgG4, PRN_ADNP, PT_ADNP, PT_IgG3, TT_ADNP, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7
Standard deviation 1.482 1.233 1.102 0.908 0.723 0.689 0.495
Proportion of Variance 0.314 0.217 0.173 0.118 0.075 0.068 0.035
Cumulative Proportion 0.314 0.531 0.705 0.822 0.897 0.965 1.000

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 3 PC1: p=.22
Infant AP vs. WP boosted RCluster_ 3 PC2: p=.095

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 TT UMAP1: p=.81
Infant AP vs. WP boosted TT UMAP2: p=.031

Response Cluster: 4

Features: DT_IgG2, FHA_IgG2, FHA_IgG4, PRN_IgG2, PRN_IgG4, PT_IgG2, PT_IgG4, TT_IgG2, TT_IgG4, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9
Standard deviation 2.307 0.968 0.849 0.781 0.719 0.643 0.435 0.400 0.363
Proportion of Variance 0.591 0.104 0.080 0.068 0.057 0.046 0.021 0.018 0.015
Cumulative Proportion 0.591 0.695 0.775 0.843 0.901 0.947 0.968 0.985 1.000

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 4 PC1: p<.0001
Infant AP vs. WP boosted RCluster_ 4 PC2: p=.83

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 TT UMAP1: p<.0001
Infant AP vs. WP boosted TT UMAP2: p<.0001

Response Cluster: 5

Features: DT_IgG3, FHA_ADCP, FHA_IgG3, PRN_ADCP, PRN_IgG3, TT_ADCP, TT_IgG3, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7
Standard deviation 1.540 1.358 0.868 0.799 0.745 0.671 0.622
Proportion of Variance 0.339 0.264 0.108 0.091 0.079 0.064 0.055
Cumulative Proportion 0.339 0.602 0.710 0.801 0.880 0.945 1.000

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 5 PC1: p=.042
Infant AP vs. WP boosted RCluster_ 5 PC2: p=.44

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 TT UMAP1: p=.54
Infant AP vs. WP boosted TT UMAP2: p=.24

Response Cluster: 6

Features: FHA_ADNP, FHA_FcgR2a, FHA_FcgR3b, PRN_FcgR2a, PRN_FcgR3b, PT_ADCP, PT_FcgR2a, PT_FcgR3b, TT_FcgR3b, NA

Proportion of Variance

summary for first 5 principal components (PC)
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9
Standard deviation 2.159 1.202 0.974 0.840 0.808 0.526 0.431 0.281 0.209
Proportion of Variance 0.518 0.160 0.105 0.078 0.073 0.031 0.021 0.009 0.005
Cumulative Proportion 0.518 0.679 0.784 0.862 0.935 0.966 0.986 0.995 1.000

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 6 PC1: p=.58
Infant AP vs. WP boosted RCluster_ 6 PC2: p=.00014

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 TT UMAP1: p=.59
Infant AP vs. WP boosted TT UMAP2: p=.0038

Response Cluster: NA

Features: NA


sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.1.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] e1071_1.7-16         glue_1.8.0           RPostgres_1.4.7     
 [4] magrittr_2.0.3       broom.helpers_1.17.0 broom_1.0.7         
 [7] RColorBrewer_1.1-3   skimr_2.1.5          rmarkdown_2.28      
[10] papeR_1.0-5          xtable_1.8-4         car_3.1-3           
[13] carData_3.0-5        corrplot_0.94        rempsyc_0.1.8       
[16] FactoMineR_2.11      factoextra_1.0.7     rstatix_0.7.2       
[19] umap_0.2.10.0        pracma_2.4.4         PCAmixdata_3.1      
[22] qgraph_1.9.8         kableExtra_1.4.0     gtsummary_2.0.3     
[25] gtExtras_0.5.0       gt_0.11.1            ggfortify_0.4.17    
[28] ggpubr_0.6.0         ggExtra_0.10.1       ggrepel_0.9.6       
[31] janitor_2.2.0        here_1.0.1           data.table_1.16.2   
[34] DT_0.33              DBI_1.2.3            fpc_2.2-13          
[37] lubridate_1.9.3      forcats_1.0.0        stringr_1.5.1       
[40] dplyr_1.1.4          purrr_1.0.2          readr_2.1.5         
[43] tidyr_1.3.1          tibble_3.2.1         ggplot2_3.5.1       
[46] tidyverse_2.0.0     

loaded via a namespace (and not attached):
  [1] splines_4.4.2        later_1.3.2          rpart_4.1.23        
  [4] lifecycle_1.0.4      rprojroot_2.0.4      lattice_0.22-6      
  [7] prabclus_2.3-4       MASS_7.3-61          flashClust_1.01-2   
 [10] backports_1.5.0      Hmisc_5.1-3          sass_0.4.9          
 [13] jquerylib_0.1.4      yaml_2.3.10          httpuv_1.6.15       
 [16] flexmix_2.3-19       askpass_1.2.1        reticulate_1.39.0   
 [19] pbapply_1.7-2        multcomp_1.4-26      abind_1.4-8         
 [22] quadprog_1.5-8       TH.data_1.1-2        nnet_7.3-19         
 [25] sandwich_3.1-1       git2r_0.33.0         gmodels_2.19.1      
 [28] gdata_3.0.0          RSpectra_0.16-2      svglite_2.1.3       
 [31] codetools_0.2-20     xml2_1.3.6           tidyselect_1.2.1    
 [34] farver_2.1.2         stats4_4.4.2         base64enc_0.1-3     
 [37] jsonlite_1.8.9       Formula_1.2-5        survival_3.7-0      
 [40] emmeans_1.10.4       systemfonts_1.1.0    tools_4.4.2         
 [43] Rcpp_1.0.13          mnormt_2.1.1         gridExtra_2.3       
 [46] xfun_0.48            withr_3.0.1          fastmap_1.2.0       
 [49] fansi_1.0.6          openssl_2.2.2        digest_0.6.37       
 [52] timechange_0.3.0     R6_2.5.1             mime_0.12           
 [55] estimability_1.5.1   colorspace_2.1-1     gtools_3.9.5        
 [58] jpeg_0.1-10          diptest_0.77-1       utf8_1.2.4          
 [61] generics_0.1.3       corpcor_1.6.10       robustbase_0.99-4-1 
 [64] class_7.3-22         htmlwidgets_1.6.4    scatterplot3d_0.3-44
 [67] whisker_0.4.1        pkgconfig_2.0.3      gtable_0.3.5        
 [70] modeltools_0.2-23    blob_1.2.4           workflowr_1.7.1     
 [73] htmltools_0.5.8.1    lavaan_0.6-19        multcompView_0.1-10 
 [76] scales_1.3.0         leaps_3.2            png_0.1-8           
 [79] snakecase_0.11.1     knitr_1.48.1         rstudioapi_0.16.0   
 [82] tzdb_0.4.0           reshape2_1.4.4       coda_0.19-4.1       
 [85] checkmate_2.3.2      nlme_3.1-166         proxy_0.4-27        
 [88] repr_1.1.7           zoo_1.8-12           cachem_1.1.0        
 [91] parallel_4.4.2       miniUI_0.1.1.1       foreign_0.8-87      
 [94] pillar_1.9.0         grid_4.4.2           vctrs_0.6.5         
 [97] promises_1.3.0       cluster_2.1.6        htmlTable_2.4.3     
[100] paletteer_1.6.0      evaluate_1.0.1       pbivnorm_0.6.0      
[103] mvtnorm_1.3-1        cli_3.6.3            compiler_4.4.2      
[106] rlang_1.1.4          ggsignif_0.6.4       labeling_0.4.3      
[109] fdrtool_1.2.18       mclust_6.1.1         rematch2_2.1.2      
[112] plyr_1.8.9           fs_1.6.4             stringi_1.8.4       
[115] psych_2.4.6.26       viridisLite_0.4.2    munsell_0.5.1       
[118] Matrix_1.7-1         hms_1.1.3            glasso_1.11         
[121] bit64_4.5.2          shiny_1.9.1          highr_0.11          
[124] kernlab_0.9-33       fontawesome_0.5.2    igraph_2.0.3        
[127] bslib_0.8.0          bit_4.5.0            DEoptimR_1.1-3