Last updated: 2026-07-05

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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
    Ignored:    figures/final-selected/bits/Figure 1/.DS_Store
    Ignored:    figures/final-selected/bits/Figure 2/.DS_Store
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    Ignored:    figures/generated/.DS_Store
    Ignored:    figures/generated/Figure 5/
    Ignored:    figures/generated/Figure 7/
    Ignored:    figures/generated/Figure 8/
    Ignored:    figures/generated/Figure 9/

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/ExtendedDataTable2_GP_AUC_lineage.R:

# Extended Data Table 2: GP AUC by lineage.
#
# One row per GP (GP1..GP200), one column per major lineage (annotation_level1:
# CD8, CD4, Treg, gdT, CD8aa, Tz, DN, DP), holding the one-vs-rest AUC for
# predicting membership in that lineage from the GP's loading. Restricted to
# healthy non-thymocyte cells (the *_no_thymocytes_healthy AUC family, same as
# Figure 2/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")

level_1_AUC_list <- readRDS(paste0(data_path, "level_1_AUC_list_figure_no_thymocytes_healthy.rds"))

gp_auc_lineage <- auc_list_to_gp_table(level_1_AUC_list)

write.csv(
  gp_auc_lineage,
  file = paste0(output_path, "ExtendedDataTable2_GP_AUC_lineage.csv"),
  row.names = FALSE
)

Table

Showing the first 20 rows (of 200); download the full table at figures/generated/ExtendedDataTable2_GP_AUC_lineage.csv.

GP CD8 CD4 Treg gdT CD8aa Tz DN DP
GP1 0.590 0.592 0.512 0.721 0.704 0.555 0.560 0.608
GP2 0.522 0.562 0.522 0.527 0.577 0.529 0.544 0.506
GP3 0.608 0.555 0.610 0.789 0.761 0.554 0.542 0.551
GP4 0.534 0.513 0.531 0.519 0.515 0.536 0.524 0.591
GP5 0.533 0.525 0.521 0.499 0.507 0.533 0.531 0.532
GP6 0.573 0.495 0.689 0.586 0.592 0.548 0.597 0.500
GP7 0.508 0.539 0.516 0.589 0.503 0.537 0.531 0.519
GP8 0.520 0.507 0.522 0.515 0.531 0.570 0.518 0.566
GP9 0.516 0.526 0.524 0.499 0.508 0.541 0.566 0.608
GP10 0.530 0.557 0.505 0.549 0.512 0.524 0.523 0.596
GP11 0.500 0.526 0.505 0.546 0.528 0.525 0.524 0.505
GP12 0.541 0.542 0.657 0.506 0.527 0.660 0.539 0.509
GP13 0.560 0.557 0.562 0.552 0.571 0.554 0.575 0.505
GP14 0.518 0.516 0.510 0.535 0.539 0.532 0.511 0.560
GP15 0.570 0.583 0.533 0.522 0.533 0.546 0.575 0.550
GP16 0.507 0.504 0.552 0.513 0.559 0.513 0.556 0.543
GP17 0.537 0.534 0.535 0.521 0.513 0.512 0.498 0.497
GP18 0.554 0.570 0.529 0.497 0.543 0.574 0.502 0.500
GP19 0.509 0.530 0.551 0.509 0.507 0.735 0.546 0.610
GP20 0.528 0.546 0.503 0.518 0.552 0.517 0.528 0.530

Extended Data Table 2. One row per GP, one column per major lineage (annotation_level1). Each value is the one-vs-rest AUC for predicting membership in that lineage from the GP’s loading, computed on healthy non-thymocyte cells.


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