Last updated: 2026-07-27
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immgenT-GP-analysis/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | adaef21 | Ziang Zhang | 2026-07-27 | Build site: panel fixes and PDF-derived assets |
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| Rmd | 0fc11c3 | Ziang Zhang | 2026-07-05 | Make Extended Data Tables interactive (DT); rename Table 1’s signature columns |
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Produced by script/ExtendedDataTable6_protein_factor_matrix.R:
# Extended Data Table 6: protein factor matrix.
#
# The final processed CITE-seq protein factor matrix used by Figure 6 (panel 6b
# heatmap), exported as a plain table: one row per GP (GP1..GP200), one column
# per protein, holding the protein's factor score in that GP. Built exactly as
# script/Figure6.R (lines 58-65) does from the projected protein EBMF fit --
# drop isotype / THY1.1 / excluded / non-"good" proteins, then scale each GP
# column so its maximum absolute score is 1 (the same max|.|=1 normalization the
# heatmap uses). See code/pipeline/04_protein_projection.R for how the raw
# protein factor matrix is fit, and code/R/citeseq_shared_setup.R:35-40 for the
# protein-selection filters reproduced here.
#
# The r-object orientation is proteins x GPs; we transpose to GP x protein so GP
# is the row, as requested for the table.
data_path <- "data/"
output_path <- "figures/final-selected/"
Protein_flash_result <- readRDS(paste0(data_path, "protein_flash_selected_summary_lognorm_backfit200.rds"))
Protein_F_pm_raw <- Protein_flash_result$F_pm
# Protein-selection filters (mirror code/R/citeseq_shared_setup.R:35-40)
isotype_proteins <- grep("^Isotype", rownames(Protein_F_pm_raw), value = TRUE)
proteins_quality <- read.csv(paste0(data_path, "TableS4_citeseq_qc_20250513.csv"), header = TRUE, stringsAsFactors = FALSE, skip = 1)
good_proteins <- c(proteins_quality$protein[proteins_quality$classification == "good"], "IL2RA.CD25", "ITB7", "CD69")
exclude_proteins <- c("CD19", "CD34", "CD45.1", "CD45.2", "CD138", "TCRVA2", "TER119")
thy11_proteins <- grep("THY1.1", rownames(Protein_F_pm_raw), value = TRUE)
# Filter + per-GP-column max|.|=1 scaling (mirror script/Figure6.R:58-65)
Protein_F_pm <- Protein_F_pm_raw[!rownames(Protein_F_pm_raw) %in% isotype_proteins, ]
Protein_F_pm <- Protein_F_pm[rownames(Protein_F_pm) %in% good_proteins, ]
Protein_F_pm <- Protein_F_pm[!rownames(Protein_F_pm) %in% exclude_proteins, ]
Protein_F_pm <- Protein_F_pm[!rownames(Protein_F_pm) %in% thy11_proteins, ]
D_lognorm <- diag(1 / apply(Protein_F_pm, 2, function(x) max(abs(x))))
Protein_F_pm <- Protein_F_pm %*% D_lognorm
colnames(Protein_F_pm) <- paste0("GP", seq_len(ncol(Protein_F_pm)))
Protein_F_pm[is.na(Protein_F_pm)] <- 0
# Transpose to GP (row) x protein (column) and write out.
protein_factor_gp <- as.data.frame(t(Protein_F_pm), check.names = FALSE, stringsAsFactors = FALSE)
protein_factor_gp <- data.frame(GP = rownames(protein_factor_gp), protein_factor_gp,
check.names = FALSE, stringsAsFactors = FALSE)
rownames(protein_factor_gp) <- NULL
write.csv(
protein_factor_gp,
file = paste0(output_path, "ExtendedDataTable6_protein_factor_matrix.csv"),
row.names = FALSE
)All 200 rows and every protein column 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-protein box to filter by score
range. Scroll horizontally to see all protein columns. Download the raw
CSV at figures/final-selected/ExtendedDataTable6_protein_factor_matrix.csv.
Extended Data Table 6. The final processed CITE-seq protein factor matrix used by Figure 6 (panel 6b), as a plain table: one row per GP, one column per protein, holding the protein’s factor score in that GP. Built from the projected protein EBMF fit, restricted to the selected “good” proteins (isotype / THY1.1 / excluded proteins removed) and scaled so each GP column has maximum absolute score 1.
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