Last updated: 2026-07-28
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immgenT-GP-analysis/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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
)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