Last updated: 2026-09-10

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Knit directory: immgenT-GP-analysis/analysis/

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File Version Author Date Message
html 936ed6e Ziang Zhang 2026-09-10 Build site: Extended Data 2d without the DP lineage
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
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 cbcec52 Ziang Zhang 2026-07-30 Build site: Extended Data Figure naming
html ac650a0 Ziang Zhang 2026-07-30 Build site: Figure S5 (ex-S6a) and Figure S6 as a-f
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
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 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 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/ExtendedDataTable5_GP_AUC_tissue.R:

# Extended Data Table 5: GP AUC by tissue.
#
# One row per GP (GP1..GP200), one column per tissue (organ_simplified: blood,
# spleen, LN, bone marrow, lung, liver, ...), holding the one-vs-rest AUC for
# predicting membership in that tissue from the GP's loading. Restricted to
# healthy non-thymocyte cells (the *_no_thymocytes_healthy AUC family, same as
# Figure 3/Figure 5), extracted directly from the precomputed AUC matrices -- see
# code/pipeline/02_compute_auc.R.
#
# The AUC file's $auc is a categories x GPs matrix with raw "K##" GP names;
# auc_list_to_gp_table() transposes it to a per-GP table and relabels K -> GP.

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

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

organ_simplified_AUC_list <- readRDS(paste0(data_path, "organ_simplified_AUC_list_figure_no_thymocytes_healthy.rds"))

gp_auc_tissue <- auc_list_to_gp_table(organ_simplified_AUC_list)

write_table_xlsx(
  gp_auc_tissue,
  file = paste0(output_path, "ExtendedDataTable5_GP_AUC_tissue.xlsx"),
  sheet = "AUC by tissue"
)

Table

All 200 rows and every tissue column are browsable below: sort by clicking a column header, type a GP name into the search box under the GP column, or use a per-tissue box to filter by AUC range. Scroll horizontally to see all tissue columns. Download the workbook at figures/final-selected/ExtendedDataTable5_GP_AUC_tissue.xlsx.

Extended Data Table 5. AUC score separating cells of each tissue from all others using GP loadings (computed in tissues at baseline).


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