Last updated: 2026-08-06
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immgenT-GP-analysis/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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/ExtendedDataTable2_gene_signature_matrix.R:
# Extended Data Table 2: gene signature per GP.
#
# The comprehensive signature gene list behind Extended Data Table 1's Top
# Genes +/- columns, as a tidy long table: one row per gene, with gene_symbol,
# signature_name (GP + direction, underscore-joined, e.g. "GP1_up"), and score.
# Every gene has |score| > 0.1 on the same max|.|=1-per-GP-scaled gene factor
# matrix Table 1 uses, ranked by |score| within direction and capped at the top
# 100 up- and top 100 down-regulated genes per GP.
#
# Required inputs (data/) -- see code/README.md's "Data provenance" table.
data_path <- "data/"
output_path <- "figures/final-selected/"
source("code/R/gene_signature_helpers.R")
source("code/R/table_xlsx.R")
F_pm_filtered <- readRDS(paste0(data_path, "F_pm_filtered.rds"))
# Normalize so each GP column has max|score| = 1 (same normalization Extended
# Data Table 1 uses for its gene signatures).
F_pm_filtered <- apply(F_pm_filtered, 2, function(x) x / max(abs(x)))
# F_pm_filtered's raw columns ("F1".."F200") are already in the same factor
# order as L_pm_filtered's "K1".."K200" (same underlying flashier fit --
# 01b_filter_cells.R only filters L's rows/cells, never F's columns), so
# column i is simply GPi; no cross-matrix name matching needed here.
n_gp <- ncol(F_pm_filtered)
gp_labels <- paste0("GP", seq_len(n_gp))
gp_blocks <- build_gp_gene_signature_blocks(F_pm_filtered, cutoff = 0.1, cap = 100, annotate_truncation = FALSE)
long_table <- do.call(rbind, Map(function(gp, block) {
data.frame(
gene_symbol = block$Gene,
signature_name = paste0(gp, "_", block$Direction),
score = block$Score,
stringsAsFactors = FALSE
)
}, gp_labels, gp_blocks))
rownames(long_table) <- NULL
write_table_xlsx(
long_table,
file = paste0(output_path, "ExtendedDataTable2_gene_signature_matrix.xlsx"),
sheet = "Gene signatures"
)One row per signature gene: sort by clicking a column header, or use
the search boxes under each header to filter (e.g. type
GP1_up into the signature_name box, or a
gene symbol into gene_symbol). Download the workbook at
figures/final-selected/ExtendedDataTable2_gene_signature_matrix.xlsx.
Extended Data Table 2. The signature gene list for
every GP, as a tidy long table: one row per gene, with
signature_name identifying the GP and direction it is a
signature gene for (e.g. GP1_up) and score
its factor loading. Every gene has |score| > 0.1 on the same
max|.|=1-per-GP-scaled gene factor matrix Extended Data Table 1 uses, ranked by
|score| within each GP-direction and capped at the top 100 up- and top
100 down-regulated genes per GP. Table 1’s Top Genes
+/- columns are this table’s top 15 per direction; this table
is the full list.
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] 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