Last updated: 2026-09-04

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Knit directory: immgenT-GP-analysis/analysis/

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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/FigureS6.Rmd) and HTML (docs/FigureS6.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 0267e5b Ziang Zhang 2026-09-04 Captions from the published manuscript; trim editor notes off the page code
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 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 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 7fb2ab0 Ziang Zhang 2026-07-28 Build site: FigureS6 gallery code shows the verified-install write
html f781754 Ziang Zhang 2026-07-28 Build site: FigureS6 caption on omitted unthresholded markers
Rmd aeb91c8 Ziang Zhang 2026-07-28 Panel titles list only the markers the gate actually applied
html 3d96bb2 Ziang Zhang 2026-07-28 Build site: FigureS6 header note on the curated threshold file
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.
Rmd 91ee059 Ziang Zhang 2026-07-26 Select each panel’s code block by name, not by line number
html 91ee059 Ziang Zhang 2026-07-26 Select each panel’s code block by name, not by line number
html 92021bf Ziang Zhang 2026-07-02 Build site.
Rmd db7a5cd Ziang Zhang 2026-07-02 Recover 3 data-provenance gaps into pipeline scripts
html 827c89b Ziang Zhang 2026-07-02 Build site.
Rmd 8ac7f9f Ziang Zhang 2026-07-02 Add data provenance notes to each script; remove conversational
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

This single-panel figure is produced by script/FigureS6.R, which shares its CITE-seq setup and protein filters with Figure 6 and Extended Data Figure 7 via code/R/citeseq_shared_setup.R. The code below is shown for reference (not re-executed on this page, since the shared setup takes about a minute to load); the image is its pre-rendered output.

Setup

library(dplyr)
library(pheatmap)
library(Matrix) # protein matrices are dgCMatrix; must be attached for `[` to dispatch

data_path <- "data/"
figure_path <- "figures/final-selected/Figure S6/"
source("code/R/citeseq_shared_setup.R")

# Record when this run started, to assert at the end that the panel is newer.
run_started_at <- Sys.time()

Protein-program heatmap

# ============================================================
# s6: sparse protein-program heatmap, contamination GPs removed
# ============================================================
# The normalized protein matrix is derived here rather than in
# citeseq_shared_setup.R because this is its only consumer among the figures.
Protein_F_pm <- Protein_F_pm_raw[!rownames(Protein_F_pm_raw) %in% isotype_proteins, ]
Protein_F_pm <- Protein_F_pm[rownames(Protein_F_pm) %in% good_proteins, ]
Protein_F_pm <- Protein_F_pm[!rownames(Protein_F_pm) %in% exclude_proteins, ]
Protein_F_pm <- Protein_F_pm[!rownames(Protein_F_pm) %in% thy11_proteins, ]
D_lognorm <- diag(1 / apply(Protein_F_pm, 2, function(x) max(abs(x))))
Protein_F_pm <- Protein_F_pm %*% D_lognorm
colnames(Protein_F_pm) <- paste0("GP", 1:ncol(Protein_F_pm))
Protein_F_pm[is.na(Protein_F_pm)] <- 0

threshold_simplified <- 0
keep_rows_simplified <- apply(Protein_F_pm, 1, function(v) any(abs(v) > threshold_simplified, na.rm = TRUE))
Protein_F_pm_simplified <- Protein_F_pm[keep_rows_simplified, , drop = FALSE]
keep_cols_simplified <- apply(Protein_F_pm_simplified, 2, function(v) any(abs(v) > threshold_simplified, na.rm = TRUE))
Protein_F_pm_simplified <- Protein_F_pm_simplified[, keep_cols_simplified, drop = FALSE]

GP_contamination <- c("GP40", "GP50", "GP55", "GP188")
Protein_F_pm_simplified_no_contamination <- Protein_F_pm_simplified[, !colnames(Protein_F_pm_simplified) %in% GP_contamination, drop = FALSE]

sparse_cutoff <- 0.5
bk_sparse <- unique(c(seq(-1, -sparse_cutoff, length.out = 26), seq(-sparse_cutoff, sparse_cutoff, length.out = 51), seq(sparse_cutoff, 1, length.out = 26)))
cols_sparse <- c(colorRampPalette(c("#4575B4", "white"))(25), rep("white", 50), colorRampPalette(c("white", "#D73027"))(25))

# Display proteins as rows and GPs as columns. Order GP columns from most to
# fewest visible proteins. Order protein rows by their rightmost visible GP, so
# proteins extending into the sparse right side appear first and form a
# triangular boundary. Visible count and a rarity-weighted support score provide
# deterministic secondary ordering.
wide_matrix_s6 <- as.matrix(Protein_F_pm_simplified_no_contamination)
wide_visible_mask_s6 <- abs(wide_matrix_s6) >= sparse_cutoff
wide_gp_visible_count_s6 <- colSums(wide_visible_mask_s6)
wide_protein_visible_count_s6 <- rowSums(wide_visible_mask_s6)
wide_gp_number_s6 <- as.integer(sub("^GP", "", colnames(wide_matrix_s6)))

wide_gp_order_s6 <- order(-wide_gp_visible_count_s6, wide_gp_number_s6)
wide_mask_ordered_cols_s6 <- wide_visible_mask_s6[
  ,
  wide_gp_order_s6,
  drop = FALSE
]
wide_rightmost_visible_gp_s6 <- apply(
  wide_mask_ordered_cols_s6,
  1,
  function(values) max(which(values))
)
wide_rarity_weights_s6 <- seq_len(ncol(wide_mask_ordered_cols_s6))^2
wide_protein_rarity_score_s6 <- as.numeric(
  wide_mask_ordered_cols_s6 %*% wide_rarity_weights_s6
)
wide_protein_order_s6 <- order(
  -wide_rightmost_visible_gp_s6,
  -wide_protein_visible_count_s6,
  -wide_protein_rarity_score_s6,
  rownames(wide_matrix_s6)
)
wide_ordered_matrix_s6 <- wide_matrix_s6[
  wide_protein_order_s6,
  wide_gp_order_s6,
  drop = FALSE
]

pdf(paste0(figure_path, "s6.pdf"), width = 48, height = 14)
pheatmap::pheatmap(
  wide_ordered_matrix_s6,
  main = sprintf(
    paste0(
      "Protein programs - GP columns, triangular-first protein rows ",
      "(|score| >= %.1f; protein-row sparsity is not monotone)"
    ),
    sparse_cutoff
  ),
  color = cols_sparse,
  breaks = bk_sparse,
  cluster_rows = FALSE,
  cluster_cols = FALSE,
  border_color = "grey75",
  fontsize = 16,
  fontsize_row = 16,
  fontsize_col = 16,
  angle_col = 90,
  legend_breaks = c(-1, -sparse_cutoff, 0, sparse_cutoff, 1),
  legend_labels = c("-1", "-0.5", "0 (white)", "0.5", "1")
)
dev.off()

Version Author Date
19c977f Ziang Zhang 2026-09-02

Extended Data Fig. 6. Heatmap of scaled protein scores for each GP. We focused on the 47 proteins that performed best in the immgenT CITE-seq dataset. Seventeen GPs lacked meaningful protein correlates and were omitted.


sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.6.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] en_CA/en_CA/en_CA/C/en_CA/en_CA

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] vctrs_0.7.3     cli_3.6.6       knitr_1.50      rlang_1.2.0    
 [5] xfun_0.55       stringi_1.8.9   otel_0.2.0      promises_1.5.0 
 [9] jsonlite_2.0.0  workflowr_1.7.2 glue_1.8.1      rprojroot_2.1.1
[13] git2r_0.36.2    htmltools_0.5.9 httpuv_1.6.16   sass_0.4.10    
[17] rmarkdown_2.30  evaluate_1.0.5  jquerylib_0.1.4 tibble_3.3.0   
[21] fastmap_1.2.0   yaml_2.3.12     lifecycle_1.0.5 whisker_0.4.1  
[25] stringr_1.6.0   compiler_4.5.1  fs_1.6.6        Rcpp_1.1.1-1.1 
[29] pkgconfig_2.0.3 later_1.4.4     digest_0.6.39   R6_2.6.1       
[33] pillar_1.11.1   magrittr_2.0.5  bslib_0.9.0     tools_4.5.1    
[37] cachem_1.1.0