Last updated: 2026-08-05
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Knit directory:
immgenT-GP-analysis/analysis/
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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 4a.
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")
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.csv(
GP_activation_summary,
file = paste0(output_path, "ExtendedDataTable4_GP_during_activation.csv"),
row.names = FALSE
)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 raw CSV
at figures/final-selected/ExtendedDataTable4_GP_during_activation.csv.
Extended Data Table 4. One row per GP describing how
its loading changes with T-cell activation, computed separately in CD4
and CD8: mean_change_loadings (activated minus resting mean
loading), d (standardized mean difference = change / pooled
loading SD, the statistic plotted in Figure 4a), and
Ratio_CD8_CD4 (ratio of the CD8 to 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_1.8.7 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