ImmunopipeWSNoTCR.config.toml

# With T-cell selection, but no TCR data
name = "ImmunopipeWSNoTCR"
outdir = "./output-ws-notcr"

[plugin_opts]
diagram_theme = "fancy"

[SampleInfo.in]
infile = [ "data/samples-notcr.txt" ]

[SampleInfo.envs.stats.Sample_Diagnosis]
group = "Diagnosis"

[SampleInfo.envs.stats.Sample_Sex_Diagnosis]
group = "Diagnosis"
each = "Sex"

[SampleInfo.envs.stats.Age_Distribution]
on = "Age"
plot = "histogram"

[SampleInfo.envs.stats.Age_By_Diagnosis]
on = "Age"
group = "Diagnosis"

[SeuratPreparing.envs]
cell_qc = "nFeature_RNA > 200 & percent.mt < 5"

[TCellSelection.envs]
indicator_genes = [ "CD3E", "CD3D", "CD3G", "CD14", "CD68" ]

[ModuleScoreCalculator.envs.modules.Activation]
features = "IFNG"

[ModuleScoreCalculator.envs.modules.Proliferation]
features = "STMN1,TUBB"

[SeuratClustering.envs]
ncores = 8

[RadarPlots.envs]
by = "Diagnosis"
breakdown = "Sample"
order = [ ]

[SeuratClusterStats.envs.features_defaults]
features = "CD4,CD8A"

[SeuratClusterStats.envs.features."Violin Plots"]
kind = "violin"
pt-size = 0
devpars = { height = 500 }

[SeuratClusterStats.envs.features."Violin Plots (FOXP3, IL2RA)"]
kind = "violin"
features = [ "FOXP3", "IL2RA" ]
pt-size = 0
devpars = { height = 500 }

[ClusterMarkers.envs]
ncores = 8
dbs = [ "KEGG_2021_Human" ]

[TopExpressingGenes.envs]
dbs = [ "KEGG_2021_Human" ]

[ScFGSEA.envs]
group-by = "Diagnosis"
ident-1 = "Colitis"
ident-2 = "Control"
each = "seurat_clusters"
gmtfile = "data/MSigDB_Hallmark_v7.5.1.gmt"

[MarkersFinder.envs]
ident-1 = "Colitis"
group-by = "Diagnosis"
dbs = [ "KEGG_2021_Human" ]
overlap = [ "DEFAULT" ]

[MarkersFinder.envs.cases.c1]
subset = 'seurat_clusters == "c1"'

[MarkersFinder.envs.cases.c2]
subset = 'seurat_clusters == "c2"'

[MetaMarkers.envs]
ncores = 8
group-by = "Diagnosis"
each = "seurat_clusters"
dbs = [ "KEGG_2021_Human" ]

[ScrnaMetabolicLandscape]
gmtfile = "data/KEGG_metabolism.short.gmt"
grouping = "seurat_clusters"
grouping_prefix = "Cluster"
subsetting = "Diagnosis"

  [ScrnaMetabolicLandscape.subsetting_comparison]
  Colitis_vs_Control = [ "Colitis", "Control" ]

[MetabolicFeaturesIntraSubset.plugin_opts]
report_paging = 5