Last updated: 2026-09-10
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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. |
| 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 |
| 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/ExtendedDataTable4_GP_during_activation.R:
# Extended Data Table 4: GP activity during activation.
#
# One row per GP (GP1..GP200) summarizing how each GP's loading changes with
# T-cell activation, computed separately in CD4 and CD8: the mean change in
# loading (activated minus resting), the standardized mean difference d
# (= change / pooled loading SD; see code/R/activation_shared_setup.R's
# std_mean_diff), and the CD8/CD4 ratio of the mean loading changes. These are
# the `GP_activation_summary` quantities behind Figure 5a.
library(dplyr)
data_path <- "data/"
output_path <- "figures/final-selected/"
source("code/R/plot_utils.R") # scale_cols(), used by activation_shared_setup.R
source("code/R/setup_data.R")
source("code/R/table_xlsx.R")
gp_data <- load_gp_data(data_path = data_path)
L_pm_filtered <- gp_data$L_pm_filtered
F_pm_filtered <- gp_data$F_pm_filtered
seurat_meta_filtered <- gp_data$seurat_meta_filtered
source("code/R/activation_shared_setup.R") # -> diff_factors_merged, d_factors_merged
GP_activation_summary <- diff_factors_merged %>%
dplyr::inner_join(d_factors_merged %>% dplyr::select(SYMBOL, d_CD4, d_CD8), by = "SYMBOL") %>%
dplyr::mutate(Ratio_CD8_CD4 = mean_change_loadings_CD8 / mean_change_loadings_CD4) %>%
dplyr::select(
GP = SYMBOL,
mean_change_loadings_CD4, mean_change_loadings_CD8,
d_CD4, d_CD8,
Ratio_CD8_CD4
)
write_table_xlsx(
GP_activation_summary,
file = paste0(output_path, "ExtendedDataTable4_GP_during_activation.xlsx"),
sheet = "GP during activation"
)All 200 rows 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-column box to filter by value range. Download the workbook
at figures/final-selected/ExtendedDataTable4_GP_during_activation.xlsx.
Extended Data Table 4. Change in GP loading with T cell activation, computed in CD4 and CD8 cells separately: the mean loading in activated minus resting cells; d_CD4 and d_CD8, the corresponding standardized differences, each divided by the s.d. of the GP’s loading across all activated and resting CD4 and CD8 cells; and Ratio_CD8_CD4, the ratio of the CD8 to the CD4 mean loading change.
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