Last updated: 2026-09-10

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Knit directory: immgenT-GP-analysis/analysis/

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File Version Author Date Message
Rmd dca7ffb Ziang Zhang 2026-09-10 Strip the code-narrating prose from every page; fold code chunks by default
html 54718c4 Ziang Zhang 2026-09-10 Build site: the four mean-loading heatmaps without their titles
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
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html 3fc3789 Ziang Zhang 2026-07-27 Republish all 24 pages
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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"
)

Table

Download: 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