Principle Components Analysis - Infant Ap vs. WP

Excluding ELISA-based total IgG - Not Standardized - 7 response clusters

workflowr

• Summary
• Checks
• Past versions

Last updated: 2024-11-25

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: 5dae9d3

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 5dae9d3. 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/

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_nosigg_apwp_noEL7.Rmd) and HTML (docs/loop_pca_nosigg_apwp_noEL7.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	8de194a	alecbuetow	2024-11-25	added supervised clusters
html	8de194a	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.

---

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

Antigen: PT

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

Proportion of Variance

Summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	2.386	1.249	0.815	0.731	0.695
Proportion of Variance	0.569	0.156	0.066	0.053	0.048
Cumulative Proportion	0.569	0.725	0.792	0.845	0.893

Past versions of loop_set-1.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-2.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated PT PC1: p=.00068
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

Past versions of loop_set-3.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-4.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-5.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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_IgG3, FHA_ADCP, FHA_ADNP, FHA_FcgR2a, FHA_FcgR3b, FHA_IgG, FHA_IgG1, FHA_IgG2, FHA_IgG4

Proportion of Variance

Summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	2.367	1.104	0.926	0.820	0.705
Proportion of Variance	0.560	0.122	0.086	0.067	0.050
Cumulative Proportion	0.560	0.682	0.768	0.835	0.885

Past versions of loop_set-6.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-7.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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

Past versions of loop_set-8.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-9.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-10.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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_IgG3, PRN_ADCP, PRN_ADNP, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG, PRN_IgG1, PRN_IgG2, PRN_IgG4

Proportion of Variance

Summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	2.350	1.164	0.966	0.789	0.754
Proportion of Variance	0.552	0.135	0.093	0.062	0.057
Cumulative Proportion	0.552	0.688	0.781	0.843	0.900

Past versions of loop_set-11.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-12.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated PRN PC1: p<.0001
Infant AP vs. WP vaccinated PRN PC2: p=.12

Plot of PCA Eigen Vectors

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

Past versions of loop_set-13.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-14.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-15.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated PRN UMAP1: p=.0036
Infant AP vs. WP vaccinated PRN UMAP2: p<.0001

Antigen: DT

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

Proportion of Variance

Summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	2.035	1.210	1.143	0.956	0.860
Proportion of Variance	0.414	0.146	0.131	0.091	0.074
Cumulative Proportion	0.414	0.560	0.691	0.783	0.856

Past versions of loop_set-16.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-17.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated DT PC1: p=.00052
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

Past versions of loop_set-18.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-19.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-20.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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_IgG3, TT_ADCP, TT_ADNP, TT_FcgR2a, TT_FcgR3b, TT_IgG, TT_IgG1, TT_IgG2, TT_IgG4

Proportion of Variance

Summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	2.209	1.314	0.984	0.829	0.671
Proportion of Variance	0.488	0.173	0.097	0.069	0.045
Cumulative Proportion	0.488	0.661	0.758	0.826	0.871

Past versions of loop_set-21.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-22.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated TT PC1: p=.033
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

Past versions of loop_set-23.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-24.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-25.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.017
Infant AP vs. WP vaccinated TT UMAP2: p=.00035

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	2.414	0.984	0.880	0.757	0.734	0.605	0.590	0.541	0.408	0.384
Proportion of Variance	0.583	0.097	0.077	0.057	0.054	0.037	0.035	0.029	0.017	0.015
Cumulative Proportion	0.583	0.679	0.757	0.814	0.868	0.905	0.939	0.969	0.985	1.000

Past versions of loop_set-26.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-27.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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=.1

Plot of PCA Eigen Vectors

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

Past versions of loop_set-28.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-29.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-30.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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	1.705	0.973	0.770	0.650	0.361
Proportion of Variance	0.581	0.189	0.119	0.084	0.026
Cumulative Proportion	0.581	0.771	0.889	0.974	1.000

Past versions of loop_set-31.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-32.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster ADCD PC1: p=.24
Infant AP vs. WP vaccinated Feature Cluster ADCD PC2: p=.037

Plot of PCA Eigen Vectors

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

Past versions of loop_set-33.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-34.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-35.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.16
Infant AP vs. WP vaccinated TT UMAP2: p<.0001

Feature Cluster: ADNP / ADCP

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

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	PC9	PC10
Standard deviation	1.506	1.380	1.196	1.134	1.014	0.805	0.703	0.667	0.531	0.463
Proportion of Variance	0.227	0.190	0.143	0.129	0.103	0.065	0.049	0.044	0.028	0.021
Cumulative Proportion	0.227	0.417	0.560	0.689	0.792	0.856	0.906	0.950	0.979	1.000

Past versions of loop_set-36.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-37.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster ADNP / ADCP PC1: p=.8
Infant AP vs. WP vaccinated Feature Cluster ADNP / ADCP PC2: p=.37

Plot of PCA Eigen Vectors

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

Past versions of loop_set-38.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-39.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-40.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.75
Infant AP vs. WP vaccinated TT UMAP2: p=.28

Feature Cluster: FcgR2a / FcgR3b

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

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	PC9	PC10
Standard deviation	1.928	1.408	1.353	1.138	0.865	0.521	0.234	0.210	0.185	0.140
Proportion of Variance	0.372	0.198	0.183	0.130	0.075	0.027	0.005	0.004	0.003	0.002
Cumulative Proportion	0.372	0.570	0.753	0.883	0.958	0.985	0.990	0.995	0.998	1.000

Past versions of loop_set-41.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-42.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster FcgR2a / FcgR3b PC1: p<.0001
Infant AP vs. WP vaccinated Feature Cluster FcgR2a / FcgR3b PC2: p=.00081

Plot of PCA Eigen Vectors

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

Past versions of loop_set-43.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-44.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-45.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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

Feature Cluster: IgG1

Features: PT_IgG1, FHA_IgG1, PRN_IgG1, TT_IgG1, DT_IgG1

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	1.479	0.984	0.970	0.691	0.651
Proportion of Variance	0.438	0.194	0.188	0.095	0.085
Cumulative Proportion	0.438	0.632	0.820	0.915	1.000

Past versions of loop_set-46.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-47.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster IgG1 PC1: p=.0098
Infant AP vs. WP vaccinated Feature Cluster IgG1 PC2: p=.47

Plot of PCA Eigen Vectors

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

Past versions of loop_set-48.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-49.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-50.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p<.0001
Infant AP vs. WP vaccinated TT UMAP2: p=.0083

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	1.692	0.878	0.756	0.711	0.537
Proportion of Variance	0.573	0.154	0.114	0.101	0.058
Cumulative Proportion	0.573	0.727	0.841	0.942	1.000

Past versions of loop_set-51.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-52.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated Feature Cluster IgG3 PC1: p=.0082
Infant AP vs. WP vaccinated Feature Cluster IgG3 PC2: p=.79

Plot of PCA Eigen Vectors

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

Past versions of loop_set-53.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-54.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-55.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.013
Infant AP vs. WP vaccinated TT UMAP2: p=.00097

Feature Cluster: IgG

Features: PT_IgG, FHA_IgG, PRN_IgG, TT_IgG, DT_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

Past versions of loop_set-56.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-57.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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

Past versions of loop_set-58.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-59.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-60.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p<.0001
Infant AP vs. WP vaccinated TT UMAP2: p=.00023

Response Cluster: 1

Features: DT_ADCD, DT_ADCP, DT_ADNP, FHA_ADCD, PRN_ADCD, TT_ADCD

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6
Standard deviation	1.708	1.062	0.932	0.714	0.667	0.361
Proportion of Variance	0.486	0.188	0.145	0.085	0.074	0.022
Cumulative Proportion	0.486	0.674	0.819	0.904	0.978	1.000

Past versions of loop_set-61.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-62.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 1 PC1: p=.53
Infant AP vs. WP vaccinated RCluster_ 1 PC2: p=.36

Plot of PCA Eigen Vectors

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

Past versions of loop_set-63.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-64.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-65.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.0018
Infant AP vs. WP vaccinated TT UMAP2: p=.07

Response Cluster: 2

Features: DT_IgG3, FHA_IgG3, PRN_IgG3, PT_ADCD, PT_ADCP, PT_ADNP, PT_FcgR2a, PT_FcgR3b, PT_IgG, PT_IgG1, PT_IgG3, TT_IgG3

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	PC9	PC10	PC11	PC12
Standard deviation	2.477	1.444	0.856	0.826	0.753	0.653	0.640	0.573	0.489	0.474	0.380	0.150
Proportion of Variance	0.511	0.174	0.061	0.057	0.047	0.036	0.034	0.027	0.020	0.019	0.012	0.002
Cumulative Proportion	0.511	0.685	0.746	0.803	0.850	0.886	0.920	0.947	0.967	0.986	0.998	1.000

Past versions of loop_set-66.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-67.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 2 PC1: p=.0015
Infant AP vs. WP vaccinated RCluster_ 2 PC2: p=.43

Plot of PCA Eigen Vectors

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

Past versions of loop_set-68.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-69.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-70.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.18
Infant AP vs. WP vaccinated TT UMAP2: p=.00011

Response Cluster: 3

Features: FHA_ADCP, FHA_ADNP, FHA_FcgR2a, FHA_FcgR3b, FHA_IgG, FHA_IgG1

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6
Standard deviation	2.015	0.897	0.674	0.605	0.506	0.243
Proportion of Variance	0.676	0.134	0.076	0.061	0.043	0.010
Cumulative Proportion	0.676	0.811	0.886	0.947	0.990	1.000

Past versions of loop_set-71.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-72.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 3 PC1: p<.0001
Infant AP vs. WP vaccinated RCluster_ 3 PC2: p=.00026

Plot of PCA Eigen Vectors

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

Past versions of loop_set-73.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-74.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-75.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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: 4

Features: PRN_ADCP, PRN_ADNP, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG, PRN_IgG1

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6
Standard deviation	2.021	0.949	0.748	0.540	0.313	0.254
Proportion of Variance	0.681	0.150	0.093	0.049	0.016	0.011
Cumulative Proportion	0.681	0.831	0.924	0.973	0.989	1.000

Past versions of loop_set-76.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-77.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 4 PC1: p=.00014
Infant AP vs. WP vaccinated RCluster_ 4 PC2: p=1

Plot of PCA Eigen Vectors

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

Past versions of loop_set-78.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-79.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-80.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.13
Infant AP vs. WP vaccinated TT UMAP2: p=.00044

Response Cluster: 5

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

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6
Standard deviation	2.043	0.790	0.654	0.577	0.525	0.407
Proportion of Variance	0.696	0.104	0.071	0.056	0.046	0.028
Cumulative Proportion	0.696	0.800	0.871	0.926	0.972	1.000

Past versions of loop_set-81.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-82.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 5 PC1: p=.016
Infant AP vs. WP vaccinated RCluster_ 5 PC2: p=.54

Plot of PCA Eigen Vectors

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

Past versions of loop_set-83.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-84.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-85.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.062
Infant AP vs. WP vaccinated TT UMAP2: p=.032

Response Cluster: 6

Features: DT_FcgR2a, DT_FcgR3b, DT_IgG, DT_IgG1

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4
Standard deviation	1.713	0.804	0.571	0.305
Proportion of Variance	0.733	0.162	0.082	0.023
Cumulative Proportion	0.733	0.895	0.977	1.000

Past versions of loop_set-86.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-87.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 6 PC1: p=.045
Infant AP vs. WP vaccinated RCluster_ 6 PC2: p=.57

Plot of PCA Eigen Vectors

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

Past versions of loop_set-88.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-89.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-90.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP vaccinated TT UMAP1: p=.082
Infant AP vs. WP vaccinated TT UMAP2: p=.11

Response Cluster: 7

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	2.414	0.984	0.880	0.757	0.734	0.605	0.590	0.541	0.408	0.384
Proportion of Variance	0.583	0.097	0.077	0.057	0.054	0.037	0.035	0.029	0.017	0.015
Cumulative Proportion	0.583	0.679	0.757	0.814	0.868	0.905	0.939	0.969	0.985	1.000

Past versions of loop_set-91.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-92.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP vaccinated RCluster_ 7 PC1: p<.0001
Infant AP vs. WP vaccinated RCluster_ 7 PC2: p=.1

Plot of PCA Eigen Vectors

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

Past versions of loop_set-93.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-94.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-95.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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

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

Antigen: PT

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

Proportion of Variance

Summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	2.076	1.378	1.022	0.852	0.820
Proportion of Variance	0.431	0.190	0.104	0.073	0.067
Cumulative Proportion	0.431	0.621	0.725	0.798	0.865

Past versions of loop_set-96.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-97.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted PT PC1: p=.97
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

Past versions of loop_set-98.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-99.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-100.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted PT UMAP1: p=.77
Infant AP vs. WP boosted PT UMAP2: p<.0001

Antigen: FHA

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

Proportion of Variance

Summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	2.331	1.044	0.975	0.859	0.738
Proportion of Variance	0.543	0.109	0.095	0.074	0.055
Cumulative Proportion	0.543	0.652	0.747	0.821	0.876

Past versions of loop_set-101.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-102.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted FHA PC1: p<.0001
Infant AP vs. WP boosted FHA PC2: p=.0081

Plot of PCA Eigen Vectors

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

Past versions of loop_set-103.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-104.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-105.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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

Antigen: PRN

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

Proportion of Variance

Summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	2.243	1.139	1.027	0.956	0.813
Proportion of Variance	0.503	0.130	0.105	0.091	0.066
Cumulative Proportion	0.503	0.633	0.738	0.830	0.896

Past versions of loop_set-106.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-107.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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

Past versions of loop_set-108.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-109.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-110.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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

Antigen: DT

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

Proportion of Variance

Summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	1.859	1.202	1.117	1.037	0.979
Proportion of Variance	0.345	0.144	0.125	0.108	0.096
Cumulative Proportion	0.345	0.490	0.615	0.722	0.818

Past versions of loop_set-111.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-112.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted DT PC1: p=.28
Infant AP vs. WP boosted DT PC2: p=.0046

Plot of PCA Eigen Vectors

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

Past versions of loop_set-113.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-114.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-115.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted DT UMAP1: p<.0001
Infant AP vs. WP boosted DT UMAP2: p=.038

Antigen: TT

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

Proportion of Variance

Summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	1.788	1.408	1.110	0.967	0.889
Proportion of Variance	0.320	0.198	0.123	0.094	0.079
Cumulative Proportion	0.320	0.518	0.641	0.735	0.814

Past versions of loop_set-116.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-117.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted TT PC1: p=.00033
Infant AP vs. WP boosted TT PC2: p=.00013

Plot of PCA Eigen Vectors

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

Past versions of loop_set-118.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-119.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-120.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p<.0001
Infant AP vs. WP boosted TT UMAP2: p=.001

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	2.446	0.979	0.920	0.818	0.735	0.594	0.511	0.409	0.367	0.295
Proportion of Variance	0.598	0.096	0.085	0.067	0.054	0.035	0.026	0.017	0.013	0.009
Cumulative Proportion	0.598	0.694	0.779	0.846	0.900	0.935	0.961	0.978	0.991	1.000

Past versions of loop_set-121.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-122.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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=.33

Plot of PCA Eigen Vectors

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

Past versions of loop_set-123.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-124.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-125.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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	1.893	0.796	0.577	0.555	0.378
Proportion of Variance	0.717	0.127	0.066	0.062	0.029
Cumulative Proportion	0.717	0.843	0.910	0.971	1.000

Past versions of loop_set-126.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-127.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster ADCD PC1: p=.46
Infant AP vs. WP boosted Feature Cluster ADCD PC2: p=.0013

Plot of PCA Eigen Vectors

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

Past versions of loop_set-128.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-129.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-130.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.21
Infant AP vs. WP boosted TT UMAP2: p=.95

Feature Cluster: ADNP / ADCP

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

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	PC9	PC10
Standard deviation	1.638	1.363	1.295	0.971	0.921	0.866	0.705	0.570	0.499	0.409
Proportion of Variance	0.268	0.186	0.168	0.094	0.085	0.075	0.050	0.033	0.025	0.017
Cumulative Proportion	0.268	0.454	0.622	0.716	0.801	0.876	0.926	0.958	0.983	1.000

Past versions of loop_set-131.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-132.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster ADNP / ADCP PC1: p=.29
Infant AP vs. WP boosted Feature Cluster ADNP / ADCP PC2: p=.014

Plot of PCA Eigen Vectors

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

Past versions of loop_set-133.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-134.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-135.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.62
Infant AP vs. WP boosted TT UMAP2: p=.0087

Feature Cluster: FcgR2a / FcgR3b

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

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	PC9	PC10
Standard deviation	1.727	1.506	1.331	1.088	0.909	0.819	0.339	0.327	0.226	0.153
Proportion of Variance	0.298	0.227	0.177	0.118	0.083	0.067	0.012	0.011	0.005	0.002
Cumulative Proportion	0.298	0.525	0.702	0.821	0.903	0.970	0.982	0.993	0.998	1.000

Past versions of loop_set-136.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-137.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster FcgR2a / FcgR3b PC1: p=.00064
Infant AP vs. WP boosted Feature Cluster FcgR2a / FcgR3b PC2: p=.18

Plot of PCA Eigen Vectors

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

Past versions of loop_set-138.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-139.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-140.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.23
Infant AP vs. WP boosted TT UMAP2: p<.0001

Feature Cluster: IgG1

Features: FHA_IgG1, PRN_IgG1, PT_IgG1, DT_IgG1, TT_IgG1

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	1.591	0.935	0.872	0.707	0.578
Proportion of Variance	0.506	0.175	0.152	0.100	0.067
Cumulative Proportion	0.506	0.681	0.833	0.933	1.000

Past versions of loop_set-141.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-142.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster IgG1 PC1: p=.2
Infant AP vs. WP boosted Feature Cluster IgG1 PC2: p=.00019

Plot of PCA Eigen Vectors

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

Past versions of loop_set-143.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-144.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-145.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.0031
Infant AP vs. WP boosted TT UMAP2: p=.2

Feature Cluster: IgG3

Features: PT_IgG3, DT_IgG3, FHA_IgG3, PRN_IgG3, TT_IgG3

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	1.584	0.939	0.771	0.750	0.673
Proportion of Variance	0.502	0.176	0.119	0.112	0.091
Cumulative Proportion	0.502	0.678	0.797	0.909	1.000

Past versions of loop_set-146.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-147.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted Feature Cluster IgG3 PC1: p=.053
Infant AP vs. WP boosted Feature Cluster IgG3 PC2: p=.55

Plot of PCA Eigen Vectors

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

Past versions of loop_set-148.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-149.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-150.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.035
Infant AP vs. WP boosted TT UMAP2: p=.034

Feature Cluster: IgG

Features: FHA_IgG, PRN_IgG, PT_IgG, DT_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

Past versions of loop_set-151.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-152.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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

Past versions of loop_set-153.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-154.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-155.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.0064
Infant AP vs. WP boosted TT UMAP2: p=.6

Response Cluster: 1

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	1.893	0.796	0.577	0.555	0.378
Proportion of Variance	0.717	0.127	0.066	0.062	0.029
Cumulative Proportion	0.717	0.843	0.910	0.971	1.000

Past versions of loop_set-156.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-157.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 1 PC1: p=.46
Infant AP vs. WP boosted RCluster_ 1 PC2: p=.0013

Plot of PCA Eigen Vectors

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

Past versions of loop_set-158.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-159.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-160.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.21
Infant AP vs. WP boosted TT UMAP2: p=.95

Response Cluster: 2

Features: DT_ADCP, DT_ADNP, TT_ADCP, TT_ADNP, TT_FcgR2a, TT_FcgR3b

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6
Standard deviation	1.527	1.171	0.968	0.770	0.709	0.516
Proportion of Variance	0.388	0.229	0.156	0.099	0.084	0.044
Cumulative Proportion	0.388	0.617	0.773	0.872	0.956	1.000

Past versions of loop_set-161.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-162.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 2 PC1: p=.00048
Infant AP vs. WP boosted RCluster_ 2 PC2: p=.92

Plot of PCA Eigen Vectors

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

Past versions of loop_set-163.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-164.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-165.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.022
Infant AP vs. WP boosted TT UMAP2: p=.013

Response Cluster: 3

Features: FHA_ADCP, FHA_ADNP, FHA_FcgR2a, FHA_FcgR3b, FHA_IgG, FHA_IgG1, PRN_ADCP, PRN_FcgR2a, PRN_FcgR3b, PRN_IgG, PRN_IgG1

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6	PC7	PC8	PC9	PC10	PC11
Standard deviation	2.488	1.310	0.956	0.849	0.691	0.596	0.560	0.441	0.250	0.184	0.160
Proportion of Variance	0.563	0.156	0.083	0.065	0.043	0.032	0.028	0.018	0.006	0.003	0.002
Cumulative Proportion	0.563	0.719	0.802	0.867	0.911	0.943	0.971	0.989	0.995	0.998	1.000

Past versions of loop_set-166.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-167.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 3 PC1: p<.0001
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

Past versions of loop_set-168.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-169.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-170.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.85
Infant AP vs. WP boosted TT UMAP2: p<.0001

Response Cluster: 4

Features: PT_ADCP, PT_FcgR2a, PT_FcgR3b, PT_IgG, PT_IgG1, PT_IgG3

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6
Standard deviation	1.941	0.886	0.764	0.693	0.533	0.311
Proportion of Variance	0.628	0.131	0.097	0.080	0.047	0.016
Cumulative Proportion	0.628	0.759	0.856	0.937	0.984	1.000

Past versions of loop_set-171.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-172.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 4 PC1: p=.69
Infant AP vs. WP boosted RCluster_ 4 PC2: p=.16

Plot of PCA Eigen Vectors

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

Past versions of loop_set-173.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-174.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-175.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.39
Infant AP vs. WP boosted TT UMAP2: p=.81

Response Cluster: 5

Features: DT_FcgR2a, DT_FcgR3b, DT_IgG, DT_IgG1, DT_IgG3, PRN_ADNP, PT_ADNP

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5	PC6	PC7
Standard deviation	1.704	1.182	0.995	0.776	0.728	0.635	0.417
Proportion of Variance	0.415	0.200	0.142	0.086	0.076	0.058	0.025
Cumulative Proportion	0.415	0.614	0.756	0.842	0.918	0.975	1.000

Past versions of loop_set-176.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-177.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 5 PC1: p=.95
Infant AP vs. WP boosted RCluster_ 5 PC2: p=.05

Plot of PCA Eigen Vectors

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

Past versions of loop_set-178.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-179.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-180.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.037
Infant AP vs. WP boosted TT UMAP2: p=.97

Response Cluster: 6

Features: FHA_IgG3, PRN_IgG3, TT_IgG, TT_IgG1, TT_IgG3

Proportion of Variance

summary for first 5 principal components (PC)

	PC1	PC2	PC3	PC4	PC5
Standard deviation	1.558	1.133	0.761	0.688	0.486
Proportion of Variance	0.485	0.257	0.116	0.095	0.047
Cumulative Proportion	0.485	0.742	0.858	0.953	1.000

Past versions of loop_set-181.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-182.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 6 PC1: p=.7
Infant AP vs. WP boosted RCluster_ 6 PC2: p=.0053

Plot of PCA Eigen Vectors

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

Past versions of loop_set-183.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-184.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-185.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of UMAP loadings by arm
Infant AP vs. WP boosted TT UMAP1: p=.025
Infant AP vs. WP boosted TT UMAP2: p=.4

Response Cluster: 7

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	2.446	0.979	0.920	0.818	0.735	0.594	0.511	0.409	0.367	0.295
Proportion of Variance	0.598	0.096	0.085	0.067	0.054	0.035	0.026	0.017	0.013	0.009
Cumulative Proportion	0.598	0.694	0.779	0.846	0.900	0.935	0.961	0.978	0.991	1.000

Past versions of loop_set-186.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of PC1 vs PC2 scores

Past versions of loop_set-187.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Comparison of principle components by arm
Infant AP vs. WP boosted RCluster_ 7 PC1: p<.0001
Infant AP vs. WP boosted RCluster_ 7 PC2: p=.33

Plot of PCA Eigen Vectors

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

Past versions of loop_set-188.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

**Loadings plot

Past versions of loop_set-189.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

Plot of UMAP1 vs UMAP2 Loadings

Past versions of loop_set-190.png

Version	Author	Date
8de194a	alecbuetow	2024-11-25

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

Session information

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