Last updated: 2026-07-09
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Knit directory:
immgenT-GP-analysis/analysis/
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Produced by script/ExtendedDataTable8_gene_signature_matrix_long.R:
# Extended Data Table 8 (long format): comprehensive gene signature matrix.
#
# The same signature genes as the wide-format version
# (script/ExtendedDataTable8_gene_signature_matrix_wide.R), reshaped 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 silently capped at the top 100
# up- and top 100 down-regulated genes per GP (no truncation-count row here,
# unlike the wide version -- see
# code/R/gene_signature_helpers.R::build_gp_gene_signature_blocks()'s
# `annotate_truncation` argument).
#
# Required inputs (data/) -- see code/README.md's "Data provenance" table.
data_path <- "data/"
output_path <- "figures/generated/"
source("code/R/gene_signature_helpers.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.csv(
long_table,
file = paste0(output_path, "ExtendedDataTable8_gene_signature_matrix_long.csv"),
row.names = FALSE
)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 raw CSV at
figures/generated/ExtendedDataTable8_gene_signature_matrix_long.csv.
The same data is also available in a per-GP-column wide format.
Extended Data Table 8. The comprehensive signature
gene list for every GP, as a tidy long table: one row per gene, with
signature_name identifying the GP and direction it’s 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 5 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: Asia/Tokyo
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] stringr_1.6.0 compiler_4.5.1 fs_1.6.6 htmlwidgets_1.6.4
[29] Rcpp_1.1.1-1.1 pkgconfig_2.0.3 later_1.4.4 digest_0.6.39
[33] R6_2.6.1 pillar_1.11.1 magrittr_2.0.5 bslib_0.9.0
[37] tools_4.5.1 cachem_1.1.0