Principle Components Analysis - Maternal Tdap+ vs. mTdap-
Excluding ELISA-based total IgG - IgG Standardized - 7 response clusters
Lisa Gallagher, David Kook, Alec Buetow, Scot Zens
Last updated: 2024-12-02
Checks: 7 0
Knit directory:
madi-biostat-project3-SDY8003-Thailand/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 03a267b | alecbuetow | 2024-12-02 | updated loops with feature 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. |
| html | 9d33ff3 | f006zvn1 | 2024-08-19 | dimensionality reduction executed, pngs and html updated |
| Rmd | 5261902 | f006zvn1 | 2024-08-14 | UMAP added to dimensionality reduction for matpm analyses |
| html | 358003a | Michael S. Zens | 2024-06-18 | more supporting files for the Maternal Tdap+ vs. Tdap- |
| Rmd | ffc6428 | Michael S. Zens | 2024-06-18 | big set of maternal Tdap+ vs Tdap- results |
Maternal Tdap+ vs. Tdap- 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 | 2.158 | 1.119 | 1.000 | 0.922 | 0.862 |
| Proportion of Variance | 0.466 | 0.125 | 0.100 | 0.085 | 0.074 |
| Cumulative Proportion | 0.466 | 0.591 | 0.691 | 0.776 | 0.850 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated PT PC1: p=.00018
Maternal Tdap+ vs. Tdap- vaccinated PT PC2: p=.82
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Antigen: FHA
Features: FHA_ADCD, FHA_ADNP, FHA_FcgR2a, FHA_FcgR3b, FHA_IgG1, FHA_IgG3, FHA_ADCP, FHA_IgG, FHA_IgG2, FHA_IgG4
Proportion of Variance
Summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.936 | 1.240 | 1.072 | 1.007 | 0.840 |
| Proportion of Variance | 0.375 | 0.154 | 0.115 | 0.101 | 0.070 |
| Cumulative Proportion | 0.375 | 0.529 | 0.644 | 0.745 | 0.815 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated FHA PC1: p=.00059
Maternal Tdap+ vs. Tdap- vaccinated FHA PC2: p=.002
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Antigen: PRN
Features: PRN_ADCD, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG1, PRN_IgG3, PRN_ADCP, PRN_IgG, PRN_IgG4, PRN_ADNP, PRN_IgG2
Proportion of Variance
Summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.709 | 1.193 | 1.052 | 1.005 | 0.974 |
| Proportion of Variance | 0.292 | 0.142 | 0.111 | 0.101 | 0.095 |
| Cumulative Proportion | 0.292 | 0.434 | 0.545 | 0.646 | 0.741 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated PRN PC1: p<.0001
Maternal Tdap+ vs. Tdap- vaccinated PRN PC2: p=.082
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Antigen: DT
Features: DT_ADCD, DT_FcgR2a, DT_FcgR3b, DT_IgG1, DT_IgG3, DT_ADCP, DT_ADNP, DT_IgG, DT_IgG2, DT_IgG4
Proportion of Variance
Summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.677 | 1.283 | 1.180 | 1.093 | 0.889 |
| Proportion of Variance | 0.281 | 0.165 | 0.139 | 0.120 | 0.079 |
| Cumulative Proportion | 0.281 | 0.446 | 0.585 | 0.705 | 0.784 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated DT PC1: p<.0001
Maternal Tdap+ vs. Tdap- vaccinated DT PC2: p=.064
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Antigen: TT
Features: TT_ADCD, TT_ADCP, TT_ADNP, TT_FcgR2a, TT_FcgR3b, TT_IgG1, TT_IgG3, TT_IgG, TT_IgG2, TT_IgG4
Proportion of Variance
Summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.978 | 1.214 | 1.017 | 0.972 | 0.872 |
| Proportion of Variance | 0.391 | 0.147 | 0.103 | 0.095 | 0.076 |
| Cumulative Proportion | 0.391 | 0.539 | 0.642 | 0.737 | 0.813 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated TT PC1: p<.0001
Maternal Tdap+ vs. Tdap- vaccinated TT PC2: p=.77
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Feature Cluster: IgG2 / IgG4
Features: PT_IgG2, PRN_IgG4, DT_IgG2, DT_IgG4, FHA_IgG2, FHA_IgG4, PT_IgG4, TT_IgG2, TT_IgG4, PRN_IgG2
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 1.811 | 1.254 | 1.105 | 1.003 | 0.931 | 0.765 | 0.739 | 0.653 | 0.527 | 0.466 |
| Proportion of Variance | 0.328 | 0.157 | 0.122 | 0.101 | 0.087 | 0.059 | 0.055 | 0.043 | 0.028 | 0.022 |
| Cumulative Proportion | 0.328 | 0.485 | 0.607 | 0.708 | 0.795 | 0.853 | 0.908 | 0.950 | 0.978 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster IgG2 / IgG4 PC1:
p=.41
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster IgG2 / IgG4 PC2:
p=.12
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
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 | 1.966 | 0.772 | 0.566 | 0.350 | 0.313 |
| Proportion of Variance | 0.773 | 0.119 | 0.064 | 0.024 | 0.020 |
| Cumulative Proportion | 0.773 | 0.892 | 0.956 | 0.980 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster ADCD PC1:
p=.0038
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster ADCD PC2: p=.032
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Feature Cluster: ADNP / ADCP
Features: FHA_ADNP, PT_ADCP, PT_ADNP, TT_ADCP, TT_ADNP, DT_ADCP, FHA_ADCP, PRN_ADCP, DT_ADNP, PRN_ADNP
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 1.649 | 1.234 | 1.123 | 1.015 | 0.990 | 0.853 | 0.754 | 0.737 | 0.635 | 0.494 |
| Proportion of Variance | 0.272 | 0.152 | 0.126 | 0.103 | 0.098 | 0.073 | 0.057 | 0.054 | 0.040 | 0.024 |
| Cumulative Proportion | 0.272 | 0.424 | 0.550 | 0.653 | 0.751 | 0.824 | 0.881 | 0.935 | 0.976 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster ADNP / ADCP PC1:
p=.00032
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster ADNP / ADCP PC2:
p=.051
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Feature Cluster: FcgR2a / FcgR3b
Features: DT_FcgR2a, DT_FcgR3b, FHA_FcgR2a, FHA_FcgR3b, PRN_FcgR2a, PRN_FcgR3b, PT_FcgR2a, PT_FcgR3b, TT_FcgR2a, TT_FcgR3b
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 2.764 | 0.774 | 0.724 | 0.646 | 0.543 | 0.501 | 0.335 | 0.277 | 0.214 | 0.191 |
| Proportion of Variance | 0.764 | 0.060 | 0.052 | 0.042 | 0.029 | 0.025 | 0.011 | 0.008 | 0.005 | 0.004 |
| Cumulative Proportion | 0.764 | 0.824 | 0.877 | 0.918 | 0.948 | 0.973 | 0.984 | 0.992 | 0.996 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster FcgR2a / FcgR3b PC1:
p<.0001
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster FcgR2a / FcgR3b PC2:
p=.8
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
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 | 1.781 | 0.895 | 0.655 | 0.571 | 0.521 |
| Proportion of Variance | 0.634 | 0.160 | 0.086 | 0.065 | 0.054 |
| Cumulative Proportion | 0.634 | 0.795 | 0.880 | 0.946 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster IgG1 PC1:
p=.014
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster IgG1 PC2: p=.23
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
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 | 1.823 | 0.767 | 0.669 | 0.595 | 0.536 |
| Proportion of Variance | 0.665 | 0.118 | 0.089 | 0.071 | 0.057 |
| Cumulative Proportion | 0.665 | 0.782 | 0.872 | 0.943 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster IgG3 PC1:
p=.00052
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster IgG3 PC2: p=.66
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Feature Cluster: IgG
Features: DT_IgG, FHA_IgG, PRN_IgG, TT_IgG, PT_IgG
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.640 | 0.962 | 0.797 | 0.660 | 0.559 |
| Proportion of Variance | 0.538 | 0.185 | 0.127 | 0.087 | 0.063 |
| Cumulative Proportion | 0.538 | 0.723 | 0.850 | 0.937 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster IgG PC1:
p=.0077
Maternal Tdap+ vs. Tdap- vaccinated Feature Cluster IgG PC2:
p=.00011
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Response Cluster: 1
Features: DT_ADCD, DT_FcgR2a, DT_FcgR3b, DT_IgG1, DT_IgG3, FHA_ADCD, FHA_ADNP, FHA_FcgR2a, FHA_FcgR3b, FHA_IgG1, FHA_IgG3, PRN_ADCD, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG1, PRN_IgG3, PT_ADCD, PT_ADCP, PT_ADNP, PT_FcgR2a, PT_FcgR3b, PT_IgG1, PT_IgG3, TT_ADCD, TT_ADCP, TT_ADNP, TT_FcgR2a, TT_FcgR3b, TT_IgG1, TT_IgG3
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 | PC11 | PC12 | PC13 | PC14 | PC15 | PC16 | PC17 | PC18 | PC19 | PC20 | PC21 | PC22 | PC23 | PC24 | PC25 | PC26 | PC27 | PC28 | PC29 | PC30 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 3.843 | 1.533 | 1.391 | 1.378 | 1.111 | 1.025 | 0.962 | 0.847 | 0.808 | 0.738 | 0.689 | 0.646 | 0.639 | 0.605 | 0.569 | 0.556 | 0.524 | 0.485 | 0.452 | 0.429 | 0.365 | 0.347 | 0.311 | 0.307 | 0.277 | 0.265 | 0.239 | 0.184 | 0.170 | 0.133 |
| Proportion of Variance | 0.492 | 0.078 | 0.064 | 0.063 | 0.041 | 0.035 | 0.031 | 0.024 | 0.022 | 0.018 | 0.016 | 0.014 | 0.014 | 0.012 | 0.011 | 0.010 | 0.009 | 0.008 | 0.007 | 0.006 | 0.004 | 0.004 | 0.003 | 0.003 | 0.003 | 0.002 | 0.002 | 0.001 | 0.001 | 0.001 |
| Cumulative Proportion | 0.492 | 0.571 | 0.635 | 0.698 | 0.739 | 0.774 | 0.805 | 0.829 | 0.851 | 0.869 | 0.885 | 0.899 | 0.912 | 0.925 | 0.935 | 0.946 | 0.955 | 0.963 | 0.970 | 0.976 | 0.980 | 0.984 | 0.987 | 0.991 | 0.993 | 0.995 | 0.997 | 0.998 | 0.999 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 1 PC1: p<.0001
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 1 PC2: p=.46
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Response Cluster: 2
Features: DT_ADCP, FHA_ADCP, PRN_ADCP
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | |
|---|---|---|---|
| Standard deviation | 1.224 | 0.986 | 0.727 |
| Proportion of Variance | 0.499 | 0.324 | 0.176 |
| Cumulative Proportion | 0.499 | 0.824 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 2 PC1: p=.43
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 2 PC2: p=.81
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Response Cluster: 3
Features: DT_ADNP, PT_IgG2
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | |
|---|---|---|
| Standard deviation | 1.098 | 0.891 |
| Proportion of Variance | 0.603 | 0.397 |
| Cumulative Proportion | 0.603 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 3 PC1: p=.66
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 3 PC2: p=.29
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Response Cluster: 4
Features: DT_IgG, FHA_IgG, PRN_IgG, PRN_IgG4, TT_IgG
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.599 | 1.003 | 0.819 | 0.666 | 0.570 |
| Proportion of Variance | 0.511 | 0.201 | 0.134 | 0.089 | 0.065 |
| Cumulative Proportion | 0.511 | 0.712 | 0.846 | 0.935 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 4 PC1: p=.034
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 4 PC2: p=.28
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Response Cluster: 5
Features: DT_IgG2, DT_IgG4, FHA_IgG2, FHA_IgG4, PT_IgG4, TT_IgG2, TT_IgG4
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | |
|---|---|---|---|---|---|---|---|
| Standard deviation | 1.745 | 1.077 | 1.033 | 0.764 | 0.734 | 0.592 | 0.508 |
| Proportion of Variance | 0.435 | 0.166 | 0.152 | 0.083 | 0.077 | 0.050 | 0.037 |
| Cumulative Proportion | 0.435 | 0.601 | 0.753 | 0.836 | 0.913 | 0.963 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 5 PC1: p=.28
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 5 PC2: p=.09
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Response Cluster: 6
Features: PRN_ADNP
Response Cluster: 7
Features: PRN_IgG2, PT_IgG
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | |
|---|---|---|
| Standard deviation | 1.110 | 0.877 |
| Proportion of Variance | 0.616 | 0.384 |
| Cumulative Proportion | 0.616 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 7 PC1: p<.0001
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 7 PC2: p=.15
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
**Loadings
plot
Maternal Tdap+ vs. Tdap- visit: boosted - boosted : PCA Results
Antigen: PT
Features: PT_ADCD, PT_FcgR2a, PT_ADNP, PT_ADCP, PT_FcgR3b, PT_IgG, PT_IgG1, PT_IgG2, PT_IgG4, PT_IgG3
Proportion of Variance
Summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.539 | 1.229 | 1.086 | 1.021 | 0.959 |
| Proportion of Variance | 0.237 | 0.151 | 0.118 | 0.104 | 0.092 |
| Cumulative Proportion | 0.237 | 0.388 | 0.506 | 0.610 | 0.702 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted PT PC1: p=.76
Maternal Tdap+ vs. Tdap- boosted PT PC2: p=.036
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
**Loadings
plot
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Plot of UMAP1 vs UMAP2 Loadings
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- boosted PT UMAP1: p=.042
Maternal Tdap+ vs. Tdap- boosted PT UMAP2: p=.061
Antigen: FHA
Features: FHA_ADCD, FHA_ADNP, FHA_ADCP, FHA_FcgR2a, FHA_FcgR3b, FHA_IgG, FHA_IgG1, FHA_IgG2, FHA_IgG4, FHA_IgG3
Proportion of Variance
Summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.739 | 1.224 | 1.128 | 1.051 | 1.006 |
| Proportion of Variance | 0.303 | 0.150 | 0.127 | 0.110 | 0.101 |
| Cumulative Proportion | 0.303 | 0.452 | 0.580 | 0.690 | 0.791 |
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Plot of PC1 vs PC2 scores
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted FHA PC1: p=.3
Maternal Tdap+ vs. Tdap- boosted FHA PC2: p=.28
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
**Loadings
plot
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Plot of UMAP1 vs UMAP2 Loadings
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- boosted FHA UMAP1: p=.81
Maternal Tdap+ vs. Tdap- boosted FHA UMAP2: p=.022
Antigen: PRN
Features: PRN_ADCD, PRN_ADNP, PRN_ADCP, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG, PRN_IgG1, PRN_IgG2, PRN_IgG4, PRN_IgG3
Proportion of Variance
Summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.541 | 1.253 | 1.104 | 1.062 | 0.996 |
| Proportion of Variance | 0.237 | 0.157 | 0.122 | 0.113 | 0.099 |
| Cumulative Proportion | 0.237 | 0.394 | 0.516 | 0.629 | 0.728 |
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Plot of PC1 vs PC2 scores
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted PRN PC1: p=.8
Maternal Tdap+ vs. Tdap- boosted PRN PC2: p=.9
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
**Loadings
plot
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Plot of UMAP1 vs UMAP2 Loadings
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- boosted PRN UMAP1: p=.33
Maternal Tdap+ vs. Tdap- boosted PRN UMAP2: p=.23
Antigen: DT
Features: DT_ADCD, DT_FcgR2a, DT_ADCP, DT_ADNP, DT_FcgR3b, DT_IgG, DT_IgG1, DT_IgG2, DT_IgG4, DT_IgG3
Proportion of Variance
Summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.319 | 1.286 | 1.260 | 1.104 | 1.063 |
| Proportion of Variance | 0.174 | 0.165 | 0.159 | 0.122 | 0.113 |
| Cumulative Proportion | 0.174 | 0.339 | 0.498 | 0.620 | 0.733 |
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Plot of PC1 vs PC2 scores
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted DT PC1: p=.49
Maternal Tdap+ vs. Tdap- boosted DT PC2: p=.86
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
**Loadings
plot
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Plot of UMAP1 vs UMAP2 Loadings
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- boosted DT UMAP1: p=.42
Maternal Tdap+ vs. Tdap- boosted DT UMAP2: p=.84
Antigen: TT
Features: TT_ADCD, TT_ADCP, TT_FcgR2a, TT_IgG2, TT_ADNP, TT_FcgR3b, TT_IgG, TT_IgG1, TT_IgG4, TT_IgG3
Proportion of Variance
Summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.362 | 1.210 | 1.153 | 1.077 | 1.039 |
| Proportion of Variance | 0.185 | 0.146 | 0.133 | 0.116 | 0.108 |
| Cumulative Proportion | 0.185 | 0.332 | 0.465 | 0.581 | 0.689 |
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Plot of PC1 vs PC2 scores
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted TT PC1: p=.92
Maternal Tdap+ vs. Tdap- boosted TT PC2: p=.2
Plot of PCA Eigen Vectors
Correlation between features and each PC score - colored by
variance contribution
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
**Loadings
plot
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Plot of UMAP1 vs UMAP2 Loadings
| Version | Author | Date |
|---|---|---|
| 9d33ff3 | f006zvn1 | 2024-08-19 |
Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.62
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.35
Feature Cluster: IgG2 / IgG4
Features: TT_IgG2, DT_IgG2, DT_IgG4, FHA_IgG2, FHA_IgG4, PRN_IgG2, PRN_IgG4, PT_IgG2, PT_IgG4, TT_IgG4
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 1.848 | 1.159 | 1.096 | 1.038 | 0.913 | 0.889 | 0.668 | 0.566 | 0.547 | 0.522 |
| Proportion of Variance | 0.342 | 0.134 | 0.120 | 0.108 | 0.083 | 0.079 | 0.045 | 0.032 | 0.030 | 0.027 |
| Cumulative Proportion | 0.342 | 0.476 | 0.596 | 0.704 | 0.787 | 0.866 | 0.911 | 0.943 | 0.973 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted Feature Cluster IgG2 / IgG4 PC1:
p=.39
Maternal Tdap+ vs. Tdap- boosted Feature Cluster IgG2 / IgG4 PC2:
p=.092
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.33
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.14
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 | 1.91 | 0.782 | 0.598 | 0.521 | 0.334 |
| Proportion of Variance | 0.73 | 0.122 | 0.072 | 0.054 | 0.022 |
| Cumulative Proportion | 0.73 | 0.852 | 0.923 | 0.978 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted Feature Cluster ADCD PC1: p=.35
Maternal Tdap+ vs. Tdap- boosted Feature Cluster ADCD PC2: p=.18
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.39
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.37
Feature Cluster: ADNP / ADCP
Features: TT_ADCP, DT_ADCP, DT_ADNP, FHA_ADNP, PRN_ADNP, PT_ADNP, TT_ADNP, FHA_ADCP, PRN_ADCP, PT_ADCP
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 1.713 | 1.376 | 1.047 | 0.994 | 0.918 | 0.792 | 0.749 | 0.731 | 0.539 | 0.482 |
| Proportion of Variance | 0.293 | 0.189 | 0.110 | 0.099 | 0.084 | 0.063 | 0.056 | 0.053 | 0.029 | 0.023 |
| Cumulative Proportion | 0.293 | 0.483 | 0.592 | 0.691 | 0.775 | 0.838 | 0.894 | 0.948 | 0.977 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted Feature Cluster ADNP / ADCP PC1:
p=.58
Maternal Tdap+ vs. Tdap- boosted Feature Cluster ADNP / ADCP PC2:
p=.37
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.84
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.83
Feature Cluster: FcgR2a / FcgR3b
Features: DT_FcgR2a, PT_FcgR2a, TT_FcgR2a, DT_FcgR3b, FHA_FcgR2a, FHA_FcgR3b, PRN_FcgR2a, PRN_FcgR3b, 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 | 2.115 | 1.303 | 1.148 | 1.055 | 0.747 | 0.662 | 0.416 | 0.350 | 0.243 | 0.218 |
| Proportion of Variance | 0.447 | 0.170 | 0.132 | 0.111 | 0.056 | 0.044 | 0.017 | 0.012 | 0.006 | 0.005 |
| Cumulative Proportion | 0.447 | 0.617 | 0.749 | 0.860 | 0.916 | 0.960 | 0.977 | 0.989 | 0.995 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted Feature Cluster FcgR2a / FcgR3b PC1:
p=.58
Maternal Tdap+ vs. Tdap- boosted Feature Cluster FcgR2a / FcgR3b PC2:
p=.73
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.68
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.097
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 | 1.780 | 0.892 | 0.699 | 0.565 | 0.479 |
| Proportion of Variance | 0.634 | 0.159 | 0.098 | 0.064 | 0.046 |
| Cumulative Proportion | 0.634 | 0.793 | 0.890 | 0.954 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted Feature Cluster IgG1 PC1: p=.2
Maternal Tdap+ vs. Tdap- boosted Feature Cluster IgG1 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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.96
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.14
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 | 1.540 | 0.908 | 0.855 | 0.746 | 0.720 |
| Proportion of Variance | 0.474 | 0.165 | 0.146 | 0.111 | 0.104 |
| Cumulative Proportion | 0.474 | 0.639 | 0.785 | 0.896 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted Feature Cluster IgG3 PC1: p=.62
Maternal Tdap+ vs. Tdap- boosted Feature Cluster IgG3 PC2: p=.92
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.85
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.84
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 | 0.798 | 0.644 | 0.593 | 0.515 |
| Proportion of Variance | 0.666 | 0.127 | 0.083 | 0.070 | 0.053 |
| Cumulative Proportion | 0.666 | 0.794 | 0.877 | 0.947 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted Feature Cluster IgG PC1: p=.28
Maternal Tdap+ vs. Tdap- boosted Feature Cluster IgG PC2: p=.075
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.97
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.22
Response Cluster: 1
Features: DT_ADCD, DT_FcgR2a, FHA_ADCD, PRN_ADCD, PT_ADCD, PT_FcgR2a, TT_ADCD, TT_ADCP, TT_FcgR2a, TT_IgG2
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 2.181 | 1.156 | 0.998 | 0.956 | 0.797 | 0.649 | 0.645 | 0.500 | 0.449 | 0.269 |
| Proportion of Variance | 0.476 | 0.134 | 0.100 | 0.091 | 0.064 | 0.042 | 0.042 | 0.025 | 0.020 | 0.007 |
| Cumulative Proportion | 0.476 | 0.609 | 0.709 | 0.800 | 0.864 | 0.906 | 0.948 | 0.973 | 0.993 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted RCluster_ 1 PC1: p=.41
Maternal Tdap+ vs. Tdap- boosted RCluster_ 1 PC2: p=.22
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.48
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.52
Response Cluster: 2
Features: DT_ADCP, DT_ADNP, FHA_ADNP, PRN_ADNP, PT_ADNP, TT_ADNP
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | |
|---|---|---|---|---|---|---|
| Standard deviation | 1.529 | 1.048 | 0.927 | 0.862 | 0.752 | 0.628 |
| Proportion of Variance | 0.390 | 0.183 | 0.143 | 0.124 | 0.094 | 0.066 |
| Cumulative Proportion | 0.390 | 0.573 | 0.716 | 0.840 | 0.934 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted RCluster_ 2 PC1: p=.7
Maternal Tdap+ vs. Tdap- boosted RCluster_ 2 PC2: p=.39
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.97
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.61
Response Cluster: 3
Features: DT_FcgR3b, FHA_ADCP, FHA_FcgR2a, FHA_FcgR3b, PRN_ADCP, PRN_FcgR2a, PRN_FcgR3b, PT_ADCP, 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 | 2.094 | 1.328 | 1.033 | 0.976 | 0.853 | 0.657 | 0.543 | 0.473 | 0.297 | 0.257 |
| Proportion of Variance | 0.438 | 0.176 | 0.107 | 0.095 | 0.073 | 0.043 | 0.030 | 0.022 | 0.009 | 0.007 |
| Cumulative Proportion | 0.438 | 0.615 | 0.722 | 0.817 | 0.890 | 0.933 | 0.962 | 0.985 | 0.993 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted RCluster_ 3 PC1: p=.35
Maternal Tdap+ vs. Tdap- boosted RCluster_ 3 PC2: p=.33
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.87
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.72
Response Cluster: 4
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 | 0.798 | 0.644 | 0.593 | 0.515 |
| Proportion of Variance | 0.666 | 0.127 | 0.083 | 0.070 | 0.053 |
| Cumulative Proportion | 0.666 | 0.794 | 0.877 | 0.947 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted RCluster_ 4 PC1: p=.28
Maternal Tdap+ vs. Tdap- boosted RCluster_ 4 PC2: p=.075
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.97
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.22
Response Cluster: 5
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 | 1.780 | 0.892 | 0.699 | 0.565 | 0.479 |
| Proportion of Variance | 0.634 | 0.159 | 0.098 | 0.064 | 0.046 |
| Cumulative Proportion | 0.634 | 0.793 | 0.890 | 0.954 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted RCluster_ 5 PC1: p=.2
Maternal Tdap+ vs. Tdap- boosted RCluster_ 5 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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.96
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.14
Response Cluster: 6
Features: DT_IgG2, DT_IgG4, FHA_IgG2, FHA_IgG4, PRN_IgG2, PRN_IgG4, PT_IgG2, PT_IgG4, TT_IgG4
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | |
|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 1.823 | 1.141 | 1.039 | 0.995 | 0.900 | 0.692 | 0.635 | 0.560 | 0.546 |
| Proportion of Variance | 0.369 | 0.145 | 0.120 | 0.110 | 0.090 | 0.053 | 0.045 | 0.035 | 0.033 |
| Cumulative Proportion | 0.369 | 0.514 | 0.634 | 0.744 | 0.834 | 0.887 | 0.932 | 0.967 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted RCluster_ 6 PC1: p=.43
Maternal Tdap+ vs. Tdap- boosted RCluster_ 6 PC2: p=.044
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.79
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.12
Response Cluster: 7
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 | 1.540 | 0.908 | 0.855 | 0.746 | 0.720 |
| Proportion of Variance | 0.474 | 0.165 | 0.146 | 0.111 | 0.104 |
| Cumulative Proportion | 0.474 | 0.639 | 0.785 | 0.896 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted RCluster_ 7 PC1: p=.62
Maternal Tdap+ vs. Tdap- boosted RCluster_ 7 PC2: p=.92
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
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.85
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.84
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