Principle Components Analysis - Infant Ap vs. WP
Excluding ELISA-based total IgG - Standardized by Total IgG - 7 response clusters
Lisa Gallagher, David Kook, Alec Buetow, Scot Zens
Last updated: 2024-11-25
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Knit directory:
madi-biostat-project3-SDY8003-Thailand/
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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 | 9d33ff3 | f006zvn1 | 2024-08-19 | dimensionality reduction executed, pngs and html updated |
| html | 9d33ff3 | f006zvn1 | 2024-08-19 | dimensionality reduction executed, pngs and html updated |
| Rmd | 94fa346 | f006zvn1 | 2024-08-12 | handled cases with insufficient features, added UMAP to dimensionality reduction section |
| Rmd | 4c89856 | Michael S. Zens | 2024-06-13 | filled out covariate analysis |
| html | 4c89856 | Michael S. Zens | 2024-06-13 | filled out covariate analysis |
| Rmd | 3a1ebaf | Michael S. Zens | 2024-06-06 | Changed the basis for all dataframes - used imputation and single source in the connection.R code. |
| Rmd | dd04d76 | Michael S. Zens | 2024-05-31 | working on covariate analysis in the pca loop |
| Rmd | 5d4b6f5 | Michael S. Zens | 2024-05-14 | addressed a tanglex merge conflict |
| Rmd | db918a1 | Michael S. Zens | 2024-05-14 | fixed confounder tables and PCA function to adjust for confounders |
| html | db918a1 | Michael S. Zens | 2024-05-14 | fixed confounder tables and PCA function to adjust for confounders |
| Rmd | a738faa | Michael S. Zens | 2024-05-09 | fixed the confounding |
| html | a738faa | Michael S. Zens | 2024-05-09 | fixed the confounding |
| Rmd | ed92971 | Michael S. Zens | 2024-05-08 | added standard diff |
| 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_IgG1, PT_IgG, PT_IgG2, PT_IgG4, PT_ADCD, PT_ADCP, PT_ADNP, PT_FcgR2a, PT_FcgR3b, PT_IgG3
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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated PT UMAP1: p<.0001
Infant AP vs. WP vaccinated PT UMAP2: p<.0001
Antigen: FHA
Features: FHA_ADCD, FHA_ADCP, FHA_ADNP, 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 | 1.839 | 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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
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_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 | 1.634 | 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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated PRN UMAP1: p<.0001
Infant AP vs. WP vaccinated PRN UMAP2: p=.0023
Antigen: DT
Features: DT_ADCD, DT_FcgR2a, DT_FcgR3b, DT_ADCP, DT_ADNP, 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 | 1.640 | 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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
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_ADCP, TT_ADNP, TT_FcgR2a, TT_FcgR3b, TT_IgG, TT_IgG1, TT_IgG2, TT_IgG4, TT_IgG3
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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.003
Infant AP vs. WP vaccinated TT UMAP2: p<.0001
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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p<.0001
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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.058
Infant AP vs. WP vaccinated TT UMAP2: p=.84
Feature Cluster: ADNP / ADCP
Features: TT_ADCP, TT_ADNP, DT_ADCP, PRN_ADNP, DT_ADNP, FHA_ADCP, FHA_ADNP, PRN_ADCP, PT_ADCP, PT_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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.0027
Infant AP vs. WP vaccinated TT UMAP2: p=.18
Feature Cluster: FcgR2a / FcgR3b
Features: DT_FcgR2a, DT_FcgR3b, TT_FcgR2a, FHA_FcgR2a, FHA_FcgR3b, PRN_FcgR2a, PRN_FcgR3b, TT_FcgR3b, PT_FcgR2a, PT_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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.69
Infant AP vs. WP vaccinated TT UMAP2: p=.79
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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.72
Infant AP vs. WP vaccinated TT UMAP2: p=.74
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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.25
Infant AP vs. WP vaccinated TT UMAP2: p=.27
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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Plot of UMAP1 vs UMAP2 Loadings
Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.00025
Infant AP vs. WP vaccinated TT UMAP2: p<.0001
Response Cluster: 1
Features: DT_ADCD, DT_FcgR2a, DT_FcgR3b, FHA_ADCD, PRN_ADCD, PT_IgG1, TT_ADCD, TT_ADCP, TT_ADNP, TT_FcgR2a
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 2.310 | 1.112 | 1.044 | 0.831 | 0.695 | 0.645 | 0.564 | 0.483 | 0.355 | 0.264 |
| Proportion of Variance | 0.534 | 0.124 | 0.109 | 0.069 | 0.048 | 0.042 | 0.032 | 0.023 | 0.013 | 0.007 |
| Cumulative Proportion | 0.534 | 0.657 | 0.766 | 0.835 | 0.884 | 0.925 | 0.957 | 0.980 | 0.993 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 1 PC1: p=.45
Infant AP vs. WP vaccinated RCluster_ 1 PC2: p=.03
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 TT UMAP1: p=.28
Infant AP vs. WP vaccinated TT UMAP2: p=.38
Response Cluster: 2
Features: DT_ADCP, PRN_ADNP
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | |
|---|---|---|
| Standard deviation | 1.050 | 0.947 |
| Proportion of Variance | 0.551 | 0.449 |
| Cumulative Proportion | 0.551 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 2 PC1: p=.55
Infant AP vs. WP vaccinated RCluster_ 2 PC2: p=.86
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 TT UMAP1: p=.92
Infant AP vs. WP vaccinated TT UMAP2: p=.54
Response Cluster: 3
Features: DT_ADNP, FHA_ADCP, FHA_ADNP, PRN_ADCP
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 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 3 PC1: p=.031
Infant AP vs. WP vaccinated RCluster_ 3 PC2: p=.6
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 TT UMAP1: p=.8
Infant AP vs. WP vaccinated TT UMAP2: p=.11
Response Cluster: 4
Features: DT_IgG, FHA_FcgR2a, FHA_FcgR3b, FHA_IgG, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG, PT_IgG, TT_FcgR3b, TT_IgG
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 2.206 | 1.277 | 0.923 | 0.863 | 0.811 | 0.618 | 0.569 | 0.500 | 0.443 | 0.313 |
| Proportion of Variance | 0.487 | 0.163 | 0.085 | 0.075 | 0.066 | 0.038 | 0.032 | 0.025 | 0.020 | 0.010 |
| Cumulative Proportion | 0.487 | 0.650 | 0.735 | 0.809 | 0.875 | 0.913 | 0.946 | 0.971 | 0.990 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 4 PC1: p=.086
Infant AP vs. WP vaccinated RCluster_ 4 PC2: p<.0001
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 TT UMAP1: p=.00041
Infant AP vs. WP vaccinated TT UMAP2: p=.23
Response Cluster: 5
Features: DT_IgG1, FHA_IgG1, PRN_IgG1, TT_IgG1
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 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 5 PC1: p=.81
Infant AP vs. WP vaccinated RCluster_ 5 PC2: p=.021
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 TT UMAP1: p=.63
Infant AP vs. WP vaccinated TT UMAP2: p=.42
Response Cluster: 6
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 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 6 PC1: p<.0001
Infant AP vs. WP vaccinated RCluster_ 6 PC2: p=.063
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 TT UMAP1: p<.0001
Infant AP vs. WP vaccinated TT UMAP2: p<.0001
Response Cluster: 7
Features: DT_IgG3, FHA_IgG3, PRN_IgG3, PT_ADCD, PT_ADCP, PT_ADNP, PT_FcgR2a, PT_FcgR3b, PT_IgG3, TT_IgG3
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | PC6 | PC7 | PC8 | PC9 | PC10 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 2.166 | 1.274 | 0.862 | 0.817 | 0.741 | 0.734 | 0.675 | 0.587 | 0.551 | 0.287 |
| Proportion of Variance | 0.469 | 0.162 | 0.074 | 0.067 | 0.055 | 0.054 | 0.046 | 0.034 | 0.030 | 0.008 |
| Cumulative Proportion | 0.469 | 0.632 | 0.706 | 0.773 | 0.827 | 0.881 | 0.927 | 0.961 | 0.992 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 7 PC1: p=.2
Infant AP vs. WP vaccinated RCluster_ 7 PC2: p=.86
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 TT UMAP1: p=.092
Infant AP vs. WP vaccinated TT UMAP2: p=.11
Infant AP vs. WP visit: boosted - boosted : PCA Results
Antigen: PT
Features: PT_ADCD, PT_IgG1, PT_ADCP, PT_ADNP, PT_FcgR2a, PT_FcgR3b, PT_IgG, PT_IgG2, PT_IgG4, PT_IgG3
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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Antigen: FHA
Features: FHA_ADCD, FHA_IgG1, FHA_IgG, FHA_IgG2, FHA_IgG4, FHA_IgG3, FHA_ADNP, FHA_FcgR2a, FHA_FcgR3b, FHA_ADCP
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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Antigen: PRN
Features: PRN_ADCD, PRN_IgG1, PRN_ADNP, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG, PRN_IgG2, PRN_IgG4, PRN_IgG3, PRN_ADCP
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 |
Plot of PC1 vs PC2 scores
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
**Loadings
plot
Antigen: DT
Features: DT_ADCD, DT_ADCP, DT_ADNP, DT_IgG1, DT_FcgR2a, DT_FcgR3b, DT_IgG, DT_IgG2, DT_IgG3, DT_IgG4
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=.0065
Infant AP vs. WP boosted DT UMAP2: p=.002
Antigen: TT
Features: TT_ADCD, TT_FcgR2a, TT_IgG1, TT_ADNP, TT_FcgR3b, TT_IgG, TT_IgG2, TT_IgG4, TT_IgG3, TT_ADCP
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_IgG2, FHA_IgG2, FHA_IgG4, PRN_IgG2, PRN_IgG4, PT_IgG2, PT_IgG4, TT_IgG2, TT_IgG4, DT_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=.62
Infant AP vs. WP boosted TT UMAP2: p=.84
Feature Cluster: ADNP / ADCP
Features: DT_ADCP, DT_ADNP, PRN_ADNP, PT_ADCP, PT_ADNP, TT_ADNP, FHA_ADNP, FHA_ADCP, PRN_ADCP, TT_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=.75
Infant AP vs. WP boosted TT UMAP2: p=.39
Feature Cluster: FcgR2a / FcgR3b
Features: TT_FcgR2a, DT_FcgR2a, DT_FcgR3b, PRN_FcgR2a, PRN_FcgR3b, PT_FcgR2a, PT_FcgR3b, TT_FcgR3b, FHA_FcgR2a, FHA_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
| 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=.44
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 |
| 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 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
| 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
Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.85
Infant AP vs. WP boosted TT UMAP2: p=.33
Feature Cluster: IgG3
Features: DT_IgG3, FHA_IgG3, PRN_IgG3, TT_IgG3, PT_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=.28
Infant AP vs. WP boosted TT UMAP2: p=.1
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=.0035
Infant AP vs. WP boosted TT UMAP2: p=.28
Response Cluster: 1
Features: DT_ADCD, FHA_ADCD, PRN_ADCD, PT_ADCD, TT_ADCD, TT_FcgR2a
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=.83
Infant AP vs. WP boosted TT UMAP2: p=.85
Response Cluster: 2
Features: DT_ADCP, DT_ADNP, 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 | 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=.22
Infant AP vs. WP boosted TT UMAP2: p=.67
Response Cluster: 3
Features: DT_FcgR2a, DT_FcgR3b, DT_IgG, FHA_IgG, PRN_ADNP, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG, PT_ADCP, PT_ADNP, PT_FcgR2a, PT_FcgR3b, PT_IgG, TT_ADNP, TT_FcgR3b, TT_IgG
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard deviation | 2.563 | 1.330 | 1.272 | 1.144 | 0.998 | 0.953 | 0.843 | 0.670 | 0.592 | 0.583 | 0.509 | 0.488 | 0.428 | 0.377 | 0.319 | 0.240 |
| Proportion of Variance | 0.411 | 0.111 | 0.101 | 0.082 | 0.062 | 0.057 | 0.044 | 0.028 | 0.022 | 0.021 | 0.016 | 0.015 | 0.011 | 0.009 | 0.006 | 0.004 |
| Cumulative Proportion | 0.411 | 0.521 | 0.622 | 0.704 | 0.766 | 0.823 | 0.867 | 0.896 | 0.917 | 0.939 | 0.955 | 0.970 | 0.981 | 0.990 | 0.996 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 3 PC1: p=.035
Infant AP vs. WP boosted RCluster_ 3 PC2: p=.66
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=.012
Infant AP vs. WP boosted TT UMAP2: p<.0001
Response Cluster: 4
Features: 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 | |
|---|---|---|---|---|---|---|---|---|---|
| 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_IgG3, PRN_IgG3, TT_IgG3
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | |
|---|---|---|---|---|
| Standard deviation | 1.487 | 0.820 | 0.766 | 0.729 |
| Proportion of Variance | 0.553 | 0.168 | 0.147 | 0.133 |
| Cumulative Proportion | 0.553 | 0.721 | 0.867 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 5 PC1: p=.21
Infant AP vs. WP boosted RCluster_ 5 PC2: p=.076
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=.76
Infant AP vs. WP boosted TT UMAP2: p=.26
Response Cluster: 6
Features: DT_IgG4, FHA_ADNP, FHA_FcgR2a, FHA_FcgR3b, PT_IgG3
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | PC4 | PC5 | |
|---|---|---|---|---|---|
| Standard deviation | 1.563 | 1.086 | 0.907 | 0.699 | 0.261 |
| Proportion of Variance | 0.488 | 0.236 | 0.164 | 0.098 | 0.014 |
| Cumulative Proportion | 0.488 | 0.724 | 0.889 | 0.986 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 6 PC1: p=.0084
Infant AP vs. WP boosted RCluster_ 6 PC2: p=.53
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=.076
Infant AP vs. WP boosted TT UMAP2: p=.021
Response Cluster: 7
Features: FHA_ADCP, PRN_ADCP, TT_ADCP
Proportion of Variance
summary for first 5 principal components (PC)| PC1 | PC2 | PC3 | |
|---|---|---|---|
| Standard deviation | 1.405 | 0.765 | 0.663 |
| Proportion of Variance | 0.658 | 0.195 | 0.147 |
| Cumulative Proportion | 0.658 | 0.853 | 1.000 |
Plot of PC1 vs PC2 scores
Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 7 PC1: p=.059
Infant AP vs. WP boosted RCluster_ 7 PC2: p=.79
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=.099
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