Last updated: 2026-07-28

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Knit directory: immgenT-GP-analysis/analysis/

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File Version Author Date Message
html d538aa2 Ziang Zhang 2026-07-28 Build site: reordered Figures 6 / S6 / S3 and the new Figure 7b page
Rmd 4c07670 Ziang Zhang 2026-07-28 Reorder Figures 6, S6 and S3; make the ex-S5 figure Figure 7b
html 029b0ae Ziang Zhang 2026-07-28 Build site.
Rmd 0f5b5da Ziang Zhang 2026-07-28 Align all figure captions with captions_20260728_final.docx
html d0ebed0 Ziang Zhang 2026-07-28 Build site: Extended Data Table 7 as the manual protein threshold list
Rmd cf77f4e Ziang Zhang 2026-07-28 Extended Data Table 7: swap GP gating alignment for the manual protein thresholds
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/ExtendedDataTable7_protein_thresholds.R:

# Extended Data Table 7: manual protein positivity thresholds.
#
# One row per surface protein that carries a manually reviewed positivity
# threshold, and the hand-set value used to call a cell positive for that
# protein. A cell counts as positive when its log-normalized ADT value is
# strictly above the threshold (and negative when it is at or below), which is
# exactly how the protein gates in Figure 6, Figure S6, and the CITE-seq
# alignment scores are built.
#
# Provenance of the values: pipeline step 3 (code/pipeline/03_protein_thresholds.R)
# first fits a 2-component Gaussian mixture per protein and takes the upper edge
# of the negative component as an automatic cutoff. Those automatic cutoffs were
# then reviewed by eye against each protein's ADT histogram and replaced by the
# rounded, hand-set values collected here (column Threshold_manual of
# data/Thresholds_Selected_Proteins.csv) -- the values that
# code/R/citeseq_shared_setup.R actually loads and gates on.
#
# Note: this table is the published threshold set as loaded at run time. The
# hard-coded manual vector inside code/pipeline/03_protein_thresholds.R is a
# different curation round (only 12 of its 46 entries match the CSV), so it is
# deliberately not used here.

data_path <- "data/"
output_path <- "figures/final-selected/"

thresholds <- read.csv(
  paste0(data_path, "Thresholds_Selected_Proteins.csv"),
  header = TRUE,
  stringsAsFactors = FALSE
)
thresholds <- thresholds[, c("Protein", "Threshold_manual")]

# CD62L is thresholded at 3 in code/R/citeseq_shared_setup.R rather than in the
# CSV (pipeline step 3 leaves it out of the manually-reviewed subset), so it is
# appended here to match the threshold set the gating code actually sees.
thresholds <- rbind(
  thresholds,
  data.frame(Protein = "CD62L", Threshold_manual = 3)
)

# radix ordering so the row order is locale-independent
thresholds <- thresholds[order(thresholds$Protein, method = "radix"), ]
rownames(thresholds) <- NULL
colnames(thresholds) <- c("Protein", "Manual threshold")

write.csv(
  thresholds,
  file = paste0(output_path, "ExtendedDataTable7_protein_thresholds.csv"),
  row.names = FALSE
)

Table

All 42 rows are browsable below (default order: alphabetical by protein): sort by clicking a column header, type a protein name into the search box under the Protein column, or filter on a value range under Manual threshold. Download the raw CSV at figures/final-selected/ExtendedDataTable7_protein_thresholds.csv.

Extended Data Table 7. The surface proteins carrying a manually reviewed positivity threshold, and the hand-set value used to call a cell positive. Values are on the log-normalized ADT scale (Seurat LogNormalize, scale.factor = 3472); a cell is protein-positive when its value is strictly above the threshold and protein-negative when it is at or below. Thresholds were set by eye from each protein’s ADT distribution, starting from the automatic 2-component Gaussian-mixture cutoff of pipeline step 3 (code/pipeline/03_protein_thresholds.R) and rounding to the reviewed value listed here. These are the thresholds used by every protein gate in Figure 6 and Figure S6. Proteins outside this list have no manual threshold and are skipped when they appear in a GP marker signature (BTLA.CD272, GR1-LY6G-LY6C1-LY6C2, LY108, SLAM.CD150, THY1.2). None of the five appears in the marker signature of any GP still gated in a published panel (Fig. 6e-j, Fig. S6d-g), so no panel subtitle currently omits a marker; script/verify_gating_gps.R fails if that stops being true.


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