Matrix factorization analyses of the immgenT scRNA-seq data

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Last updated: 2026-09-10

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Knit directory: immgenT-GP-analysis/analysis/

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.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
html	59021bf	Ziang Zhang	2026-09-10	Build site: Extended Data 1-6 after removing the structure-plot figure
Rmd	c21f51f	Ziang Zhang	2026-09-10	Remove the per-lineage structure-plot figure; keep its record for Figure 4
html	60125af	Ziang Zhang	2026-09-10	Build site: Figure 4b on the shared column colours
html	88ee847	Ziang Zhang	2026-09-10	Build site: Figure 4b without the miniverse clusters
html	5874416	Ziang Zhang	2026-09-10	Build site: main Figure 4 inserted, Extended Data back to 1-7
Rmd	4307b28	Ziang Zhang	2026-09-10	New main Figure 4, and fold the cluster heatmap into Extended Data Figure 2
html	bf4f612	Ziang Zhang	2026-09-09	Build site: Extended Data back to 1-8
Rmd	6f01135	Ziang Zhang	2026-09-09	Pull the tissue figure back out of Extended Data; ED is 1-8 again
html	a7a481f	Ziang Zhang	2026-09-09	Build site: the rebuilt Figure 1d and the Extended Data renumbering
Rmd	c233cd8	Ziang Zhang	2026-09-09	Extended Data reorganisation: split the tissue/cluster figure, renumber 3-8
html	1e88d7e	Ziang Zhang	2026-09-04	Build site: published captions and titles across all 24 pages
Rmd	0267e5b	Ziang Zhang	2026-09-04	Captions from the published manuscript; trim editor notes off the page code
html	d0a4a21	Ziang Zhang	2026-09-02	Build site: overview page rebuilt
Rmd	80e1b9b	Ziang Zhang	2026-09-02	Overview page: link the RQVI companion repository, drop the numbering note
html	19c977f	Ziang Zhang	2026-09-02	Build site: Extended Data 5-7 renumbered, Figure S5 page rebuilt
Rmd	1e5721a	Ziang Zhang	2026-09-02	Extended Data 5-7 renumbered, and Figure S5 assembled as one stacked figure
html	232079e	Ziang Zhang	2026-08-27	Build site: Extended Data Figure 8 page added
Rmd	659ff00	Ziang Zhang	2026-08-27	Extended Data Figure 8: per-lineage cluster structure plots
html	dd76d38	Ziang Zhang	2026-08-19	Build site: Figure 7 and index pages rebuilt
Rmd	801dbf7	Ziang Zhang	2026-08-19	Figure 7 pages: present Figure 7 as one figure spanning EBMF and RQVI
html	eeca07b	Ziang Zhang	2026-08-05	Keep pre-refactor provenance in panel comments off the published pages
Rmd	5651d0e	Ziang Zhang	2026-08-05	Extended Data tables: reorder to six, rebuild Table 1, drop internal notes
html	dd71400	Ziang Zhang	2026-07-31	Build site: Methods section on cell filtering by total GP membership
Rmd	3f88d67	Ziang Zhang	2026-07-31	Methods: document how L_pm_filtered / F_pm_filtered are obtained
html	6926d1b	Ziang Zhang	2026-07-31	Build site: Extended Data Table 1 annotations + tabbed top-15 version
Rmd	80f61c0	Ziang Zhang	2026-07-31	Extended Data Table 1: manual annotations + longer internal version
html	cbcec52	Ziang Zhang	2026-07-30	Build site: Extended Data Figure naming
Rmd	66aa029	Ziang Zhang	2026-07-30	Name the Extended Data figures as published on the site
html	ac650a0	Ziang Zhang	2026-07-30	Build site: Figure S5 (ex-S6a) and Figure S6 as a-f
Rmd	c9b020f	Ziang Zhang	2026-07-30	Split Figure S6’s protein-program heatmap out as Figure S5
html	732ac8d	Ziang Zhang	2026-07-29	Build site: caption alignment with captions_20260729_final.docx
Rmd	8d73953	Ziang Zhang	2026-07-28	Align captions with captions_20260729_final.docx
html	ae21d37	Ziang Zhang	2026-07-28	Build site: republish after the reorder commits
html	d538aa2	Ziang Zhang	2026-07-28	Build site: reordered Figures 6 / S6 / S3 and the new Figure 7b page
Rmd	4c07670	Ziang Zhang	2026-07-28	Reorder Figures 6, S6 and S3; make the ex-S5 figure Figure 7b
html	029b0ae	Ziang Zhang	2026-07-28	Build site.
Rmd	0f5b5da	Ziang Zhang	2026-07-28	Align all figure captions with captions_20260728_final.docx
html	d0ebed0	Ziang Zhang	2026-07-28	Build site: Extended Data Table 7 as the manual protein threshold list
Rmd	cf77f4e	Ziang Zhang	2026-07-28	Extended Data Table 7: swap GP gating alignment for the manual protein thresholds
html	3fc3789	Ziang Zhang	2026-07-27	Republish all 24 pages
html	1390a03	Ziang Zhang	2026-07-27	Republish all 24 pages
html	adaef21	Ziang Zhang	2026-07-27	Build site: panel fixes and PDF-derived assets
html	5b19858	Ziang Zhang	2026-07-27	Build site.
html	9862b6d	Ziang Zhang	2026-07-23	Build site.
Rmd	98d2924	Ziang Zhang	2026-07-23	Reword Figure S5 page for a publication audience
html	9398c72	Ziang Zhang	2026-07-23	Publish Figure S5 workflowr page
Rmd	b9f4f58	Ziang Zhang	2026-07-23	Add Figure S5: EBMF vs matched-RQVI level2-cluster comparison
Rmd	b197499	Ziang Zhang	2026-07-16	Restructure main figures (renumber + split Figure 1)
html	b197499	Ziang Zhang	2026-07-16	Restructure main figures (renumber + split Figure 1)
Rmd	f0c481d	Ziang Zhang	2026-07-14	Document CITE-seq fixed-loading EBMF workflow
html	f0c481d	Ziang Zhang	2026-07-14	Document CITE-seq fixed-loading EBMF workflow
Rmd	c344aaa	Ziang Zhang	2026-07-13	Add Figure S4 mean-loading heatmaps
html	c344aaa	Ziang Zhang	2026-07-13	Add Figure S4 mean-loading heatmaps
Rmd	cba8dd4	Ziang Zhang	2026-07-12	Add Methods page: Flashier matrix factorization
html	cba8dd4	Ziang Zhang	2026-07-12	Add Methods page: Flashier matrix factorization
html	c5cbc77	Ziang Zhang	2026-07-08	Build site.
Rmd	fb8c855	Ziang Zhang	2026-07-08	Add Extended Data Table 8: comprehensive gene signature matrix (long + wide)
html	92d1365	Ziang Zhang	2026-07-05	Build site.
Rmd	d07f797	Ziang Zhang	2026-07-05	Replace Table S1/S2/S3 with 7 fully-reproducible Extended Data Tables
html	92021bf	Ziang Zhang	2026-07-02	Build site.
html	827c89b	Ziang Zhang	2026-07-02	Build site.
Rmd	f9db962	Ziang Zhang	2026-07-02	Simplify layout: drop old code/script folders, rename
html	c6e5086	Ziang Zhang	2026-07-02	Build site.
html	5a79883	Ziang Zhang	2026-07-02	Build site.
Rmd	2b0e445	Ziang Zhang	2026-07-02	Fix GitHub source links to point at the new
html	cf1d0ac	Ziang Zhang	2026-07-02	Build site.
Rmd	06b2461	Ziang Zhang	2026-07-02	Initial commit: immgenT-GP-analysis
html	06b2461	Ziang Zhang	2026-07-02	Initial commit: immgenT-GP-analysis

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This site documents the gene program (GP) factorization analysis of the ImmGen-T single-cell RNA-seq/CITE-seq data: ~200 GPs learned by empirical Bayes matrix factorization (EBMF), and how they relate to cell lineage, tissue, activation state, transcription factors, and surface protein expression.

Each page below covers one figure: for every panel, the R code that produced it, the figure itself, and its caption.

Main figures

• Figure 1: A gene-program architecture underlies T cell heterogeneity across the immgenT atlas
• Figure 2: Individual T cells deploy sparse combinations of gene programs that expand with activation
• Figure 3: T cell lineage identity is encoded by both lineage-restricted and shared gene programs
• Figure 4: Gene programs resolve T cell states below the level of lineage
• Figure 5: Activated T cell states arise from shared and lineage-biased combinations of gene programs
• Figure 6: Tissue-associated gene programs reflect both tissue adaptation and T cell subset composition
• Figure 7: Surface-marker associations are context-dependent, but combinatorial gating resolves specific gene programs
• Figure 8b: A nonlinear deep-learning framework independently recovers the immgenT gene-program landscape

Figure 8 (A nonlinear deep-learning framework independently recovers the immgenT gene-program landscape) brings the EBMF programs documented here together with RQVI, a non-linear deep-learning factorization of the same cells. Panel b, the cluster-level comparison of the two factorizations, is documented on the page above; the RQVI panels are documented in the companion repository for the RQVI framework.

Extended Data figures

• Extended Data Figure 1: GP reproducibility and batch-effect evaluation
• Extended Data Figure 2: Tz- and CD8-specific GPs (GP30 and GP58, respectively), and GP activity across T cell clusters
• Extended Data Figure 3: Activation-associated GPs
• Extended Data Figure 4: Protein programs across GPs
• Extended Data Figure 5: Surface proteins association with GP

Extended Data Figure 6 (RQVI scalability and representative matches to lineage-associated EBMF GPs) is documented in the same companion repository for the RQVI framework.

Extended Data tables

• Extended Data Table 1: GP characteristics and annotations
• Extended Data Table 2: Gene signature per GP
• Extended Data Table 3: GP association with lineages
• Extended Data Table 4: GP activity during activation
• Extended Data Table 5: GP association with tissues
• Extended Data Table 6: GP association with clusters

Methods

• Fitting EBMF using flashier (including how L_pm_filtered / F_pm_filtered are obtained by filtering cells on total GP membership)
• Fitting CITE-seq protein programs with fixed scRNA loadings

Reproducing these figures

Every page above is generated by a single R script in script/, which sources shared plotting/data-loading helpers from code/R/. To regenerate a figure yourself, run (from the repository root):

Rscript script/Figure1.R