Principle Components Analysis - Maternal Tdap+ vs. mTdap-

Last updated: 2024-12-02

Checks: 7 0

Knit directory: madi-biostat-project3-SDY8003-Thailand/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20231106)

The command set.seed(20231106) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: 03a267b

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 03a267b. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .RData
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    data/.DS_Store
    Ignored:    figure/

Unstaged changes:
    Modified:   code/pca_scores_nosigg_matpm_noEL6.RData
    Modified:   code/pca_scores_sigg_matpm_noEL7.RData
    Modified:   code/pca_scores_sigg_matpm_noIgG7.RData

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/loop_pca_sigg_matpm_noEL6.Rmd) and HTML (docs/loop_pca_sigg_matpm_noEL6.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated PT UMAP1: p<.0001
Maternal Tdap+ vs. Tdap- vaccinated PT UMAP2: p=.1

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated FHA UMAP1: p=.11
Maternal Tdap+ vs. Tdap- vaccinated FHA UMAP2: p=.094

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated PRN UMAP1: p=.67
Maternal Tdap+ vs. Tdap- vaccinated PRN UMAP2: p<.0001

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated DT UMAP1: p<.0001
Maternal Tdap+ vs. Tdap- vaccinated DT UMAP2: p=.54

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.0015
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.3

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.25
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.0099

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.036
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.0035

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.088
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p<.0001

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.00087
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p<.0001

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.033
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.029

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.021
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.0045

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.00059
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.00058

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.017
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.00012

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.76
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.93

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.25
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.1

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.84
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.029

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

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

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

**Loadings plot

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of UMAP1 vs UMAP2 Loadings

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP1: p=.33
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p=.31

Response Cluster: 6

Features: PRN_ADNP, PRN_IgG2, PT_IgG

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3
Standard deviation	1.120	0.992	0.873
Proportion of Variance	0.418	0.328	0.254
Cumulative Proportion	0.418	0.746	1.000

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Plot of PC1 vs PC2 scores

Version	Author	Date
9d33ff3	f006zvn1	2024-08-19
358003a	Michael S. Zens	2024-06-18

Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 6 PC1: p<.0001
Maternal Tdap+ vs. Tdap- vaccinated RCluster_ 6 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
358003a	Michael S. Zens	2024-06-18

**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- vaccinated TT UMAP1: p=.95
Maternal Tdap+ vs. Tdap- vaccinated TT UMAP2: p<.0001

Maternal Tdap+ vs. Tdap- visit: boosted - boosted : PCA Results

Antigen: PT

Features: PT_ADCD, PT_FcgR2a, PT_IgG1, PT_ADNP, PT_ADCP, 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	1.539	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

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 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=.27
Maternal Tdap+ vs. Tdap- boosted PT UMAP2: p=.012

Antigen: FHA

Features: FHA_ADCD, FHA_IgG1, FHA_ADNP, FHA_ADCP, FHA_FcgR2a, FHA_FcgR3b, FHA_IgG, 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=.048
Maternal Tdap+ vs. Tdap- boosted FHA UMAP2: p=.56

Antigen: PRN

Features: PRN_ADCD, PRN_IgG1, PRN_ADNP, PRN_ADCP, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG, 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=.24
Maternal Tdap+ vs. Tdap- boosted PRN UMAP2: p=.31

Antigen: DT

Features: DT_ADCD, DT_FcgR2a, DT_IgG1, DT_ADCP, DT_ADNP, DT_FcgR3b, DT_IgG, 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=.36
Maternal Tdap+ vs. Tdap- boosted DT UMAP2: p=.91

Antigen: TT

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

Plot of PC1 vs PC2 scores

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

**Loadings plot

Plot of UMAP1 vs UMAP2 Loadings

Comparison of UMAP loadings by arm
Maternal Tdap+ vs. Tdap- boosted TT UMAP1: p=.52
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.45

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, DT_IgG1, FHA_ADCD, FHA_IgG1, PRN_ADCD, PRN_IgG1, PT_ADCD, PT_FcgR2a, PT_IgG1, TT_ADCD, TT_ADCP, TT_FcgR2a, TT_IgG1, TT_IgG2

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
Standard deviation	2.243	1.773	1.160	1.078	0.985	0.814	0.738	0.720	0.636	0.539	0.500	0.479	0.467	0.402	0.259
Proportion of Variance	0.336	0.209	0.090	0.078	0.065	0.044	0.036	0.035	0.027	0.019	0.017	0.015	0.015	0.011	0.004
Cumulative Proportion	0.336	0.545	0.635	0.712	0.777	0.821	0.857	0.892	0.919	0.938	0.955	0.970	0.985	0.996	1.000

Plot of PC1 vs PC2 scores

Comparison of principle components by arm
Maternal Tdap+ vs. Tdap- boosted RCluster_ 1 PC1: p=.27
Maternal Tdap+ vs. Tdap- boosted RCluster_ 1 PC2: p=.54

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=.93
Maternal Tdap+ vs. Tdap- boosted TT UMAP2: p=.1

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_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_ 5 PC1: p=.43
Maternal Tdap+ vs. Tdap- boosted RCluster_ 5 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: 6

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_ 6 PC1: p=.62
Maternal Tdap+ vs. Tdap- boosted RCluster_ 6 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

Principle Components Analysis - Maternal Tdap+ vs. mTdap-

Excluding ELISA-based total IgG - IgG Standardized - 6 response clusters

Lisa Gallagher, David Kook, Alec Buetow, Scot Zens

Maternal Tdap+ vs. Tdap- visit:vaccinated - vaccinated : PCA Results

Antigen: PT

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Antigen: FHA

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Antigen: PRN

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Antigen: DT

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Antigen: TT

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Feature Cluster: IgG2 / IgG4

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Feature Cluster: ADCD

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Feature Cluster: ADNP / ADCP

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Feature Cluster: FcgR2a / FcgR3b

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Feature Cluster: IgG1

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Feature Cluster: IgG3

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Feature Cluster: IgG

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Response Cluster: 1

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Response Cluster: 2

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Response Cluster: 3

Proportion of Variance

Plot of PC1 vs PC2 scores

Plot of PCA Eigen Vectors

Plot of UMAP1 vs UMAP2 Loadings

Response Cluster: 4