ImmunopipeSupervised.config.toml

name = "ImmunopipeSupervised"
outdir = "./output-supervised"

[plugin_opts]
diagram_theme = "fancy"

[SampleInfo.in]
infile = [ "data/samples.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]
ncores = 4
cell_qc = "nFeature_RNA > 200 & percent.mt < 5"
doublet_detector = "DoubletFinder"

[SeuratClusteringOfAllCells.envs]
ncores = 8

  [SeuratClusteringOfAllCells.envs.FindClusters]
  resolution = 1.6

[ClusterMarkersOfAllCells.envs]
ncores = 4

[TopExpressingGenesOfAllCells]
forks = 2

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

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

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

[SeuratMap2Ref.envs]
ncores = 8
ref = "prepared-data/pbmc_multimodal_2023.rds"
use = "celltype.l2"

[SeuratMap2Ref.envs.MapQuery]
reduction-model = "wnn.umap"

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

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

[TCRClustering.envs]
# tool = "ClusTCR"  # not supported in the docker image

[TCRClusterStats.envs.shared_clusters]
heatmap_meta = [ "Diagnosis" ]

  [TCRClusterStats.envs.shared_clusters.devpars]
  width = 600
  height = 450

[TESSA.envs]
predefined_b = true
max_iter = 10

[SeuratClusterStats.envs.hists."All Clonotypes along Activation"]
x = "Activation"

[SeuratClusterStats.envs.hists."Top 10 Clonotypes along Activation"]
x = "Activation"
cells_by = "CDR3.aa"
cells_orderby = "desc(Clones)"
cells_n = 10
each = "Diagnosis"
devpars = { height = 600 }

[SeuratClusterStats.envs.stats."Composition of cell types in Colitis samples"]
subset = 'Diagnosis == "Colitis"'
circos = true
ident = "seurat_clusters"
group-by = "Sex"
circos_labels_rot = true

[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 }

[SeuratClusterStats.envs.features."TCR Clone Size"]
kind = "feature"
features = [ "Clones" ]

[SeuratClusterStats.envs.features."TCR Cluster Size"]
kind = "feature"
features = [ "TCR_Cluster_Size" ]

[Immunarch.envs.divs.cases]
Gini_Coef = { }

  [Immunarch.envs.divs.cases.Gini_Coef_in_Treg]
  subset = 'seurat_clusters == "Treg"'

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

[CloneResidency.envs.cases.M_vs_F]
subject = [ "Diagnosis" ]
group = "Sex"
order = [ "M", "F" ]

[CloneResidency.envs.cases.Diagnosis]
subject = [ "Sex" ]
group = "Diagnosis"
order = [ "Control", "NoColitis", "Colitis" ]

[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 == "Treg"'

[MarkersFinder.envs.cases.c2]
subset = 'seurat_clusters == "CD4 TEM"'

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

[CellsDistribution.envs]
cluster_orderby = "mean(Activation)"
group_by = "Diagnosis"
group_order = [ "Colitis", "NoColitis", "Control" ]
cells_by = "Top10Clones"
cells_orderby = "desc(CloneSize)"

  [CellsDistribution.envs.mutaters]
  Top10Clones = 'top(n=10, uniq = FALSE)'

  [CellsDistribution.envs.cases.Top10Clones]
  devpars = { width = 1500, height = 800 }
  hm_devpars = { width = 1250, height = 640 }

[CDR3AAPhyschem.envs]
group = "seurat_clusters"
target = "Treg"

  [CDR3AAPhyschem.envs.comparison]
  Tconv = [
    "CD8 TCM",
    "CD8 TEM",
  ]
  Treg = [
    "Treg",
    # too few Tregs, adding just for demonstration
    "CD4 TCM",
    "CD4 TEM",
  ]

[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