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
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    Ignored:    figures/generated/Figure 7/
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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/ExtendedDataTable4_GP_AUC_cluster.R:

# Extended Data Table 4: GP AUC by cluster.
#
# One row per GP (GP1..GP200), one column per sub-lineage cluster
# (annotation_level2: CD8.A, CD8.B, ..., CD4.A, ...), holding the one-vs-rest
# AUC for predicting membership in that cluster 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")

level_2_AUC_list <- readRDS(paste0(data_path, "level_2_AUC_list_figure_no_thymocytes_healthy.rds"))

gp_auc_cluster <- auc_list_to_gp_table(level_2_AUC_list)

write.csv(
  gp_auc_cluster,
  file = paste0(output_path, "ExtendedDataTable4_GP_AUC_cluster.csv"),
  row.names = FALSE
)

Table

Showing the first 20 rows (of 200) and first 10 columns; download the full table at figures/generated/ExtendedDataTable4_GP_AUC_cluster.csv.

GP CD8.A CD8.B CD8.C CD8.D CD8.E CD8.F CD8.G CD8.H CD8.I
GP1 0.594 0.655 0.563 0.514 0.554 0.619 0.491 0.539 0.630
GP2 0.537 0.576 0.522 0.593 0.547 0.529 0.630 0.613 0.624
GP3 0.588 0.615 0.551 0.639 0.658 0.631 0.715 0.536 0.504
GP4 0.518 0.591 0.512 0.524 0.534 0.547 0.594 0.538 0.502
GP5 0.509 0.523 0.543 0.522 0.498 0.520 0.505 0.567 0.545
GP6 0.588 0.580 0.568 0.496 0.676 0.675 0.588 0.616 0.686
GP7 0.525 0.509 0.595 0.627 0.567 0.533 0.602 0.557 0.504
GP8 0.508 0.526 0.620 0.548 0.576 0.559 0.547 0.519 0.486
GP9 0.532 0.610 0.580 0.531 0.571 0.510 0.577 0.517 0.560
GP10 0.522 0.516 0.666 0.550 0.634 0.690 0.769 0.921 0.972
GP11 0.576 0.754 0.615 0.565 0.552 0.556 0.586 0.533 0.638
GP12 0.567 0.533 0.855 0.570 0.630 0.714 0.494 0.610 0.506
GP13 0.521 0.564 0.574 0.546 0.633 0.614 0.677 0.599 0.645
GP14 0.531 0.509 0.589 0.554 0.536 0.553 0.547 0.527 0.563
GP15 0.554 0.554 0.669 0.928 0.756 0.893 0.635 0.547 0.578
GP16 0.522 0.573 0.601 0.507 0.532 0.979 0.531 0.522 0.535
GP17 0.513 0.531 0.504 0.508 0.536 0.531 0.546 0.556 0.680
GP18 0.525 0.594 0.630 0.654 0.550 0.553 0.610 0.547 0.579
GP19 0.541 0.512 0.538 0.654 0.588 0.522 0.615 0.593 0.585
GP20 0.508 0.562 0.542 0.535 0.599 0.621 0.632 0.514 0.530

Extended Data Table 4. One row per GP, one column per sub-lineage cluster (annotation_level2). Each value is the one-vs-rest AUC for predicting membership in that cluster from the GP’s loading, computed on healthy non-thymocyte cells. (Preview shows the first 10 of 107 cluster 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