Last updated: 2026-07-28
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Knit directory:
immgenT-GP-analysis/analysis/
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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/final-selected/"
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
)All 200 rows and every cluster column (107 sub-lineage clusters) 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-cluster box to filter by AUC range. Scroll horizontally to see all
cluster columns. Download the raw CSV at figures/final-selected/ExtendedDataTable4_GP_AUC_cluster.csv.
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.
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_1.8.7 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 crosstalk_1.2.2 evaluate_1.0.5 jquerylib_0.1.4
[21] tibble_3.3.0 fastmap_1.2.0 yaml_2.3.12 lifecycle_1.0.5
[25] whisker_0.4.1 stringr_1.6.0 compiler_4.5.1 fs_1.6.6
[29] htmlwidgets_1.6.4 Rcpp_1.1.1-1.1 pkgconfig_2.0.3 later_1.4.4
[33] digest_0.6.39 R6_2.6.1 pillar_1.11.1 magrittr_2.0.5
[37] bslib_0.9.0 tools_4.5.1 cachem_1.1.0