Table of content

Supplementary website for the Biorxiv paper, titled "Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in Black American and White American patients with TNBC". Zhu et al 2025.

Here you find the codes for generating figures and results in the paper.

Description	Script	Individual inputs
Single cell IMC clustering and spatial cell-cell interaction	single_cell_clustering	Refined.matrix_v1_TNBC_Clinical_updated_v0.txt (file) Xcen_v0_TNBC_race_reprocessed.txt (file) subset.giotto.R (file)
Race-specific cell-cell interaction (no plot)	race_specific_CCI	full.matrix.txt (file) command1.sh (file) do.one.R (file) command.sh (file) extract.py (file)
T cell exhaustion bubble plot	select.expr.Tcell.exh.module.bubble.dec27.py	curated.ea.list (file) curated.aa.list (file) GSM files (file)
ESG heatmap plot per query	step3.do.pearson.2.bygene.custom.py	"cell.type.expr.%s.%s.more.joined.txt" (file1)(file2) "order.%s.query.2.txt" % choice (file1)(file2)
Spatial expression plot per query	plot_one_across_tumor_nocbar.py	"dir_%s/Giotto_norm_expr.txt" % sample, "dir_%s/spatial/tissue_positions_list.csv" % sample (gzip file) paper.aa.list (file) paper.ea.list (file)
ESG line plot (BSW2 Validation Dataset)	dec23.plot.select.expr.2.py	"cell.type.expr.M%s.%s.more.joined.txt" % (module, race) (file1) (file2) pick_gnes_by_total.py (file) AA.list (file) EA.list (file) sEA files (gzip file) sAA files (gzip file)
Generation of ESGs per sample (no plot)	diffexpr.module.py	"dir_%s/Giotto_norm_expr.txt" % sample, "dir_%s/spatial/tissue_positions_list.csv" % sample (gzip file)
T cell exhaustion stats (no plot)	stats_across_tumor_Tcellexh.py	"dir_%s/Giotto_norm_expr.txt" % sample, "dir_%s/spatial/tissue_positions_list.csv" % sample (gzip file) paper.aa.list (file) paper.ea.list (file)
ESG line plot (Georgia Validation dataset)	plot.select.expr.2.EA.py	"cell.type.expr.M%s.%s.more.joined.txt" % (module, race) (file1)(file2) pick_gnes_by_total.py (file) AA.list (file) EA.list (file) MB files (gzip file)
BSW-discovery IMC clustering visualization	imc.tsne	frequency.kmeans.k20iter10000 (file) cytof_test.RData (file) cytof_test.aug13.RData (file)
BSW-discovery IMC race-specific cell-cell interaction landscape	do.pearson.2.good.apr17.py	uniq.clusters (file) pvalue.2 (file)
BSW-discovery IMC spatial plots showing examples of BA-specific CCIs	visualize.AA.cluster.fig2d.py	Xcen_v0_TNBC_race_reprocessed.txt (file) uniq.clusters (file) frequency.kmeans.k20iter10000.1 (file)
BSW-discovery IMC spatial plots showing examples of WA-specific CCIs	visualize.EA.cluster.fig2e.py	Xcen_v0_TNBC_race_reprocessed.txt (file) uniq.clusters (file) frequency.kmeans.k20iter10000.1 (file)
BA-, WA-Communities for BSW-discovery IMC	get_components_bsw_discovery.py	bsw.discovery (file)
BA-, WA-Communities for BSW-validation IMC	get_components_bsw_validation.py	bsw.validation (file)
BA-, WA-Communities for Roswell IMC	get_components_roswell.py	roswell (file)
BSW-discovery survival plot (prognostic significance of BA-Communities)	km2.py	survival.EA.all.module.both.h (file) survival.AA.all.module.both.h (file) patient.queries.key.attributes.complete (file) bsw.discovery.interaction.data.tar.gz (file)
BSW-discovery survival plot (prognostic significance of WA-Communities)	km2.EA.py	survival.EA.all.module.both.h (file) survival.AA.all.module.both.h (file) patient.queries.key.attributes.complete (file) bsw.discovery.interaction.data.tar.gz (file)
Roswell survival plot (prognositic significance of BA-Communities)	roswell/km2.test.py	roswell/clinical.good.10yr.txt (file) roswell/survival.EA.all.both.h (file) roswell/survival.AA.all.module.both.test.h (file) roswell/roswell.interaction.data.tar.gz (file)
Roswell survival plot (prognositic significance of WA-Communities)	roswell/km2.EA.py	roswell/clinical.good.10yr.txt (file) roswell/survival.EA.all.both.h (file) roswell/survival.AA.all.module.both.test.h (file) roswell/roswell.interaction.data.tar.gz (file)