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Knit directory: immgenT-GP-analysis/analysis/

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File Version Author Date Message
html a7a481f Ziang Zhang 2026-09-09 Build site: the rebuilt Figure 1d and the Extended Data renumbering
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 19c977f Ziang Zhang 2026-09-02 Build site: Extended Data 5-7 renumbered, Figure S5 page rebuilt
html cb1d7d2 Ziang Zhang 2026-08-06 Build site: Extended Data table pages read the .xlsx workbooks
Rmd faf2785 Ziang Zhang 2026-08-06 Extended Data tables: store as .xlsx instead of .csv
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 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
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html ae21d37 Ziang Zhang 2026-07-28 Build site: republish after the reorder commits
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Rmd ffe285c Ziang Zhang 2026-07-27 Reorganize figures/ and untrack local-only exploration notes
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)
html 362ebf9 Ziang Zhang 2026-07-05 Build site.
Rmd 0fc11c3 Ziang Zhang 2026-07-05 Make Extended Data Tables interactive (DT); rename Table 1’s signature columns
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

Produced by script/ExtendedDataTable1_GP_summary.R:

# Extended Data Table 1: summary of GP characteristics and comments.
#
# One row per GP (GP1..GP200) with:
#   - Top Genes + / Top Genes -: the top 15 up- and top 15 down-regulated genes
#     by factor score, among those with |score| > 0.1 on the max|.|=1-per-GP
#     scaled gene factor matrix (F_pm_filtered). GPs with fewer than 15
#     qualifying genes in a direction list all of them.
#   - Comments: the manual, human-written description of the GP, read from the
#     curated curation/GP_manual_annotations.csv (blank where a GP has no
#     comment).
#   - Prop. active cells: the fraction of non-thymocyte cells whose loading
#     exceeds 0.1 after scaling the GP's loading column by its maximum -- the
#     quantity Figure 2b histograms.
#   - N active genes: the number of genes with |score| > 0.25 on the
#     max|.|=1-per-GP scaled gene factor matrix -- the quantity Figure 2c
#     histograms. Note this is a stricter cutoff than the 0.1 used for the
#     signature-gene columns above.
#
# Writes figures/final-selected/ExtendedDataTable1_GP_summary.xlsx (a workbook
# rather than a .csv so the Comments column's Greek characters survive being
# opened in Excel -- see code/R/table_xlsx.R).
#
# The full signature gene list behind the Top Genes columns (up to 100 per
# direction) is Extended Data Table 2.

data_path <- "data/"
curation_path <- "curation/"
output_path <- "figures/final-selected/"

source("code/R/table_xlsx.R")

# ---- Loadings and gene factor matrix ----
# L_pm_filtered's columns are the flashier fit's "K1".."K200"; F_pm_filtered's
# are "F1".."F200". Both are in the same factor order, so position -- not name
# -- is what aligns them, and both are relabeled "GP1".."GP200" for output.
L_pm_filtered <- readRDS(paste0(data_path, "L_pm_filtered.rds"))
F_pm_filtered <- readRDS(paste0(data_path, "F_pm_filtered.rds"))
stopifnot(ncol(L_pm_filtered) == ncol(F_pm_filtered))
gp_labels <- paste0("GP", seq_len(ncol(L_pm_filtered)))

# ---- Prop. active cells (Figure 2b) ----
# Non-thymocyte cells only, matching Figure 2; each loading column is scaled by
# its own maximum before the 0.1 cut.
seurat_meta <- readRDS(paste0(data_path, "igt1_96_withtotalvi20260206_clean_ADTonly.Rds"))@meta.data
seurat_meta_filtered <- seurat_meta[rownames(L_pm_filtered), ]
rm(seurat_meta); gc()
non_thymo_cells <- seurat_meta_filtered$cellID[seurat_meta_filtered$annotation_level1 != "thymocyte"]
L_non_thymo <- L_pm_filtered[non_thymo_cells, ]
L_norm_col <- L_non_thymo / matrix(apply(L_non_thymo, 2, max),
                                   nrow = nrow(L_non_thymo), ncol = ncol(L_non_thymo),
                                   byrow = TRUE)
prop_active_cells <- colSums(L_norm_col > 1e-1) / nrow(L_norm_col)
rm(L_pm_filtered, L_non_thymo, L_norm_col); gc()

# ---- N active genes (Figure 2c) and signature genes ----
F_pm_norm <- apply(F_pm_filtered, 2, function(x) x / max(abs(x)))
colnames(F_pm_norm) <- gp_labels
n_active_genes <- colSums(abs(F_pm_norm) > 0.25)

top_signatures <- function(score_mat, gps, cutoff = 0.1, n = 15) {
  pos <- lapply(gps, function(gp) {
    vals <- score_mat[, gp]
    cand <- names(vals)[vals > cutoff]
    paste(head(cand[order(vals[cand], decreasing = TRUE)], n), collapse = "; ")
  })
  neg <- lapply(gps, function(gp) {
    vals <- score_mat[, gp]
    cand <- names(vals)[vals < -cutoff]
    paste(head(cand[order(abs(vals[cand]), decreasing = TRUE)], n), collapse = "; ")
  })
  list(pos = unlist(pos), neg = unlist(neg))
}
gene_sig <- top_signatures(F_pm_norm, gp_labels)

# ---- Manual comments (curated input; blank where a GP has no comment) ----
# Keyed by the GP*n* output labels. Insisting on an exact GP1..GP200 match means
# a renamed or dropped row fails loudly here instead of silently blanking a
# comment in the published table.
manual_comments <- read.csv(paste0(curation_path, "GP_manual_annotations.csv"),
                            stringsAsFactors = FALSE, colClasses = "character")
stopifnot(identical(manual_comments$GP, gp_labels))

supp_table <- data.frame(
  GP = gp_labels,
  `Top Genes +` = gene_sig$pos,
  `Top Genes -` = gene_sig$neg,
  Comments = trimws(manual_comments$Comments),
  `Prop. active cells` = as.numeric(prop_active_cells),
  `N active genes` = as.integer(n_active_genes),
  stringsAsFactors = FALSE,
  check.names = FALSE
)

write_table_xlsx(supp_table,
                 file = paste0(output_path, "ExtendedDataTable1_GP_summary.xlsx"),
                 sheet = "GP summary")

Table

All 200 rows are browsable below: sort by clicking a column header, use the search boxes under each header to filter (e.g. type a GP name, or a keyword like proliferation under Comments), or use the box in the top-right corner for a free-text search across every column. Download the workbook at figures/final-selected/ExtendedDataTable1_GP_summary.xlsx.

Extended Data Table 1. Characteristics of the 200 GPs: the columns show the top 15 up- and down-regulated genes with |score| > 0.1, the proportion of highly active cells (scaled loading > 0.1), and the number of highly active genes (|score| > 0.25).


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     

other attached packages:
[1] DT_0.34.0

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] readxl_1.4.5      rmarkdown_2.30    cellranger_1.1.0  crosstalk_1.2.2  
[21] evaluate_1.0.5    jquerylib_0.1.4   tibble_3.3.0      fastmap_1.2.0    
[25] yaml_2.3.12       lifecycle_1.0.5   whisker_0.4.1     stringr_1.6.0    
[29] compiler_4.5.1    fs_1.6.6          htmlwidgets_1.6.4 Rcpp_1.1.1-1.1   
[33] pkgconfig_2.0.3   later_1.4.4       digest_0.6.39     R6_2.6.1         
[37] pillar_1.11.1     magrittr_2.0.5    bslib_0.9.0       tools_4.5.1      
[41] cachem_1.1.0