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Merged
bbimber merged 4 commits into from
Feb 8, 2026
Merged

Expand phenotypes #148

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b834463
Expand phenotypes
bbimber Feb 8, 2026
df7df53
Test fix
bbimber Feb 8, 2026
ca325fe
Add ZEB2
bbimber Feb 8, 2026
b0daad9
Test fix
bbimber Feb 8, 2026
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4 changes: 3 additions & 1 deletion R/GeneModules.R
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Expand Up @@ -19,7 +19,9 @@ CalculateUCellScores <- function(seuratObj, forceRecalculate = FALSE, seed = Get
TandNK_Activation2 = GetGeneSet('TandNK_Activation.2'),
TandNK_Activation3 = GetGeneSet('TandNK_Activation.3'),
TandNK_ActivationCore = GetGeneSet('TandNK_Activation.Core'),
Cytotoxicity = GetGeneSet('Cytotoxicity'),
Cytotoxicity = GetGeneSet('Cytotoxicity.1'),
Cytotoxicity2 = GetGeneSet('Cytotoxicity.2'),
Cytotoxicity3 = GetGeneSet('Cytotoxicity.3'),
Cytotoxicity.GzmABH = GetGeneSet('Cytotoxicity.GzmABH'),
Cytotoxicity.GzmKM = GetGeneSet('Cytotoxicity.GzmKM'),
Glycolysis = GetGeneSet('Glycolysis'),
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12 changes: 7 additions & 5 deletions R/Phenotyping.R
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Expand Up @@ -65,7 +65,7 @@ PlotImmuneMarkers <- function(seuratObj, reductions = c('tsne', 'umap')) {
# TNFRSF4 = OX40
PlotMarkerSeries(seuratObj, reductions = reductions, features = c('CD4', 'SELL', 'LEF1', 'STAT1', 'CD40LG', 'GATA3', 'FOXP3', 'AQP3', 'GPR183', 'HOPX', 'ITGB2', 'AHNAK', 'ANXA1', 'TNFRSF4'), 'CD4 Phenotypic Markers')

PlotMarkerSeries(seuratObj, reductions = reductions, features = c('PRF1', 'GNLY', 'NKG7', 'GZMA','GZMB','GZMH','GZMK','GZMM'), 'Cytotoxicity')
PlotMarkerSeries(seuratObj, reductions = reductions, features = c('PRF1', 'GNLY', 'NKG7', 'GZMA','GZMB','GZMH','GZMK','GZMM', 'CTSW'), 'Cytotoxicity')

PlotMarkerSeries(seuratObj, reductions = reductions, features = c('MS4A1', 'CD79A', 'CD74', 'DRA'), 'B-cell Markers')

Expand Down Expand Up @@ -113,7 +113,7 @@ PlotImmuneMarkers <- function(seuratObj, reductions = c('tsne', 'umap')) {

# ZNF683 = HOBIT
# IKZF2 = Helios
PlotMarkerSeries(seuratObj, reductions = reductions, features = c('TBX21', 'GATA3', 'RORC', 'FOXP3', 'BCL6', 'EOMES', 'TOX', 'GATA2', 'TCF7', 'KLF2', 'NR4A1', 'LEF1', 'PRDM1', 'ID2', 'ID3', 'ZNF683', 'BHLHE40', 'EGR1', 'EGR2', 'EGR3', 'BACH2', 'IKZF2'), 'Transcription Factors')
PlotMarkerSeries(seuratObj, reductions = reductions, features = c('TBX21', 'GATA3', 'RORC', 'FOXP3', 'BCL6', 'EOMES', 'TOX', 'GATA2', 'TCF7', 'KLF2', 'NR4A1', 'LEF1', 'PRDM1', 'ID2', 'ID3', 'ZNF683', 'BHLHE40', 'EGR1', 'EGR2', 'EGR3', 'BACH2', 'IKZF2', 'ZEB2'), 'Transcription Factors')

PlotMarkerSeries(seuratObj, reductions = reductions, features = c('TIGIT', 'CTLA4', 'BTLA', 'PDCD1', 'CD274'), 'Inhibitory Markers')

Expand Down Expand Up @@ -148,7 +148,7 @@ PlotImmuneMarkers <- function(seuratObj, reductions = c('tsne', 'umap')) {

PlotMarkerSeries(seuratObj, features = c('TGFB1', 'TGFB2', 'TGFB3'), title = 'TGFB')

PlotMarkerSeries(seuratObj, features = c('TGFBR1', 'TGFBR2', 'TGFBR3'), title = 'TGFB Receptor')
PlotMarkerSeries(seuratObj, features = c('TGFBR1', 'TGFBR2', 'TGFBR3', 'ZEB2'), title = 'TGFB Receptor')

# KLRC2 = ENSMMUG00000050862
klrs <- c('KLRB1', 'KLRC1', 'KLRD1', 'KLRF1', 'KLRF2', 'KLRG1', 'KLRG2', 'KLRC2', 'KLRC3', 'KLRK1', 'ENSMMUG00000050862')
Expand Down Expand Up @@ -346,7 +346,9 @@ GetGeneSet <- function(name) {
# This is based on T-cell analysis from lung T/NK cells. This my not be precisely Memory/Naive.
.RegisterGeneSet('MemoryAndNaive', c('SELL', 'IL7R', 'LTB', 'SPOCK2', 'COTL1', 'JUNB', 'GPR183', 'CCR7', 'FUOM', 'CD7', 'PECAM1'))

.RegisterGeneSet('Cytotoxicity', c('PRF1', 'GNLY', 'NKG7', 'GZMA','GZMB','GZMH','GZMK','GZMM'))
.RegisterGeneSet('Cytotoxicity.1', c('PRF1', 'GNLY', 'NKG7', 'GZMA', 'GZMB', 'GZMH', 'GZMK', 'GZMM'))
.RegisterGeneSet('Cytotoxicity.2', c('PRF1', 'GNLY', 'GZMB', 'CTSW'))
.RegisterGeneSet('Cytotoxicity.3', c('PRF1', 'GNLY', 'GZMA', 'GZMB', 'GZMH', 'GZMK', 'GZMM', 'CTSW'))

.RegisterGeneSet('Cytotoxicity.GzmABH', c('GZMA','GZMB','GZMH'))
.RegisterGeneSet('Cytotoxicity.GzmKM', c('GZMK','GZMM'))
Expand Down Expand Up @@ -607,7 +609,7 @@ ExpandGeneList <- function(genes, verbose = TRUE) {
MakePhenotypingDotPlot <- function(seuratObj,
yField = 'ClusterNames_0.2',
scaled = T,
gene_lists = c('Cytotoxicity', 'EffectorCytokines'),
gene_lists = c('Cytotoxicity.1', 'EffectorCytokines'),
assay = "RNA",
scale.by = "size"
){
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51 changes: 0 additions & 51 deletions inst/components/PRF1_EffectorAxis.tsv
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69 changes: 0 additions & 69 deletions inst/components/TCR_EarlyStimulationComponent.tsv
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2 changes: 1 addition & 1 deletion man/MakePhenotypingDotPlot.Rd
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6 changes: 3 additions & 3 deletions tests/testthat/test-phenotyping.R
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Expand Up @@ -31,9 +31,9 @@ test_that("ScoreUsingSavedComponent works", {
expect_equal(round(min(abs(seuratObj$Test1)), 2), 0.07)
expect_equal(round(max(abs(seuratObj$Test1)), 2), 199.21)

seuratObj <- ScoreUsingSavedComponent(seuratObj, componentOrName = 'Tcell_NaiveToEffector', fieldName = 'Test2')
expect_equal(round(max(seuratObj$Test2), 2), 41.61)
expect_equal(round(min(seuratObj$Test2), 2), -6.69)
seuratObj <- ScoreUsingSavedComponent(seuratObj, componentOrName = 'Tcell_EffectorDifferentiation', fieldName = 'Test2')
expect_equal(round(max(seuratObj$Test2), 1), 52.1)
expect_equal(round(min(seuratObj$Test2), 2), -6.12)

seuratObj <- CalculateUCellScores(seuratObj)
expect_true('TandNK_Activation_UCell' %in% names(seuratObj@meta.data))
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