Last updated: 2026-07-05

Checks: 6 1

Knit directory: immgenT-GP-analysis/analysis/

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .claude/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/.Rhistory
    Ignored:    analysis/assets/.DS_Store
    Ignored:    code/.DS_Store
    Ignored:    data
    Ignored:    figures/final-selected/.DS_Store
    Ignored:    figures/final-selected/bits/.DS_Store
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Untracked files:
    Untracked:  analysis/ExtendedDataTable1.Rmd
    Untracked:  analysis/ExtendedDataTable2.Rmd
    Untracked:  analysis/ExtendedDataTable3.Rmd
    Untracked:  analysis/ExtendedDataTable4.Rmd
    Untracked:  analysis/ExtendedDataTable5.Rmd
    Untracked:  analysis/ExtendedDataTable6.Rmd
    Untracked:  analysis/ExtendedDataTable7.Rmd
    Untracked:  figures/generated/ExtendedDataTable1_GP_summary.csv
    Untracked:  figures/generated/ExtendedDataTable2_GP_AUC_lineage.csv
    Untracked:  figures/generated/ExtendedDataTable3_GP_AUC_tissue.csv
    Untracked:  figures/generated/ExtendedDataTable4_GP_AUC_cluster.csv
    Untracked:  figures/generated/ExtendedDataTable5_GP_during_activation.csv
    Untracked:  figures/generated/ExtendedDataTable6_protein_factor_matrix.csv
    Untracked:  figures/generated/ExtendedDataTable7_protein_gating.csv
    Untracked:  script/ExtendedDataTable1_GP_summary.R
    Untracked:  script/ExtendedDataTable2_GP_AUC_lineage.R
    Untracked:  script/ExtendedDataTable3_GP_AUC_tissue.R
    Untracked:  script/ExtendedDataTable4_GP_AUC_cluster.R
    Untracked:  script/ExtendedDataTable5_GP_during_activation.R
    Untracked:  script/ExtendedDataTable6_protein_factor_matrix.R
    Untracked:  script/ExtendedDataTable7_protein_gating.R
    Untracked:  tables/

Unstaged changes:
    Deleted:    analysis/TableS1.Rmd
    Modified:   analysis/index.Rmd
    Modified:   code/R/gated_protein_helpers.R
    Modified:   code/R/roc_auc.R
    Modified:   code/README.md
    Modified:   code/pipeline/02_compute_auc.R
    Deleted:    figures/generated/Supplementary_Table1_GP_summary.csv
    Modified:   script/README.md
    Deleted:    script/TableS1.R

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Produced by script/ExtendedDataTable3_GP_AUC_tissue.R:

# Extended Data Table 3: 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 4), 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/generated/"

source("code/R/roc_auc.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.csv(
  gp_auc_tissue,
  file = paste0(output_path, "ExtendedDataTable3_GP_AUC_tissue.csv"),
  row.names = FALSE
)

Table

Showing the first 20 rows (of 200) and first 10 columns; download the full table at figures/generated/ExtendedDataTable3_GP_AUC_tissue.csv.

GP blood spleen LN bone marrow lung liver peritoneal cavity colon epi small intestine epi
GP1 0.557 0.562 0.587 0.524 0.595 0.560 0.588 0.633 0.785
GP2 0.596 0.527 0.622 0.544 0.536 0.573 0.603 0.533 0.557
GP3 0.672 0.567 0.548 0.679 0.517 0.558 0.751 0.644 0.902
GP4 0.516 0.551 0.593 0.664 0.592 0.523 0.552 0.501 0.503
GP5 0.537 0.511 0.518 0.551 0.529 0.527 0.551 0.524 0.526
GP6 0.635 0.535 0.507 0.612 0.601 0.517 0.603 0.596 0.585
GP7 0.518 0.501 0.546 0.535 0.552 0.513 0.595 0.516 0.531
GP8 0.532 0.511 0.504 0.503 0.559 0.529 0.505 0.529 0.537
GP9 0.659 0.506 0.652 0.640 0.495 0.528 0.651 0.497 0.524
GP10 0.502 0.504 0.548 0.512 0.516 0.611 0.517 0.519 0.533
GP11 0.495 0.629 0.636 0.593 0.898 0.749 0.604 0.518 0.563
GP12 0.591 0.503 0.496 0.523 0.562 0.536 0.553 0.531 0.520
GP13 0.601 0.516 0.540 0.643 0.649 0.518 0.606 0.599 0.593
GP14 0.530 0.499 0.506 0.519 0.522 0.511 0.580 0.529 0.520
GP15 0.556 0.521 0.533 0.546 0.565 0.512 0.637 0.603 0.519
GP16 0.514 0.526 0.601 0.561 0.535 0.522 0.553 0.599 0.534
GP17 0.645 0.534 0.509 0.680 0.511 0.553 0.548 0.563 0.507
GP18 0.567 0.510 0.552 0.612 0.614 0.494 0.582 0.566 0.562
GP19 0.507 0.563 0.526 0.610 0.610 0.668 0.684 0.650 0.556
GP20 0.567 0.534 0.538 0.625 0.542 0.531 0.582 0.570 0.540

Extended Data Table 3. One row per GP, one column per tissue (organ_simplified). Each value is the one-vs-rest AUC for predicting membership in that tissue from the GP’s loading, computed on healthy non-thymocyte cells. (Preview shows the first 10 of 18 tissue columns.)


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: Asia/Tokyo
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_1.8.7   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 stringr_1.6.0  
[25] compiler_4.5.1  fs_1.6.6        Rcpp_1.1.1-1.1  pkgconfig_2.0.3
[29] later_1.4.4     digest_0.6.39   R6_2.6.1        pillar_1.11.1  
[33] magrittr_2.0.5  bslib_0.9.0     tools_4.5.1     cachem_1.1.0