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Abel Vertesy edited this page Nov 27, 2023 · 4 revisions

Welcome to the Seurat.utils wiki!

Analysing-ambient-RNA---background-RNA-contamination---the-soup-with-Seurat.utils

Function relationships

(of connected functions)

flowchart LR 

  whitelist.subset.ls.Seurat(whitelist.subset.ls.Seurat) --> getMetadataColumn(getMetadataColumn)
  umapHiLightSel(umapHiLightSel) --> getCellIDs.from.meta(getCellIDs.from.meta)
  transfer_labels_seurat(transfer_labels_seurat) --> clUMAP(clUMAP)
  transfer_labels_seurat(transfer_labels_seurat) --> isave.RDS(isave.RDS)
  subsetSeuObj.and.Save(subsetSeuObj.and.Save) --> xsave(xsave)
  subsetSeuObj.and.Save(subsetSeuObj.and.Save) --> getProject(getProject)
  subsetSeuObj.and.Save(subsetSeuObj.and.Save) --> subsetSeuObj(subsetSeuObj)
  seu.plot.PC.var.explained(seu.plot.PC.var.explained) --> seu.PC.var.explained(seu.PC.var.explained)
  scBarplot.CellFractions(scBarplot.CellFractions) --> shorten_clustering_names(shorten_clustering_names)
  save.parameters(save.parameters) --> ww.get.1st.Seur.element(ww.get.1st.Seur.element)
  remove_clusters_and_drop_levels(remove_clusters_and_drop_levels) --> remove.residual.small.clusters(remove.residual.small.clusters)
  remove_clusters_and_drop_levels(remove_clusters_and_drop_levels) --> dropLevelsSeurat(dropLevelsSeurat)
  remove_clusters_and_drop_levels(remove_clusters_and_drop_levels) --> GetClusteringRuns(GetClusteringRuns)
  remove.cells.by.UMAP(remove.cells.by.UMAP) --> clUMAP(clUMAP)
  regress_out_and_recalculate_seurat(regress_out_and_recalculate_seurat) --> calc.q99.Expression.and.set.all.genes(calc.q99.Expression.and.set.all.genes)
  regress_out_and_recalculate_seurat(regress_out_and_recalculate_seurat) --> qUMAP(qUMAP)
  regress_out_and_recalculate_seurat(regress_out_and_recalculate_seurat) --> SetupReductionsNtoKdimensions(SetupReductionsNtoKdimensions)
  regress_out_and_recalculate_seurat(regress_out_and_recalculate_seurat) --> clUMAP(clUMAP)
  regress_out_and_recalculate_seurat(regress_out_and_recalculate_seurat) --> GetClusteringRuns(GetClusteringRuns)
  regress_out_and_recalculate_seurat(regress_out_and_recalculate_seurat) --> isave.RDS(isave.RDS)
  recall.parameters(recall.parameters) --> ww.get.1st.Seur.element(ww.get.1st.Seur.element)
  recall.meta.tags.n.datasets(recall.meta.tags.n.datasets) --> ww.get.1st.Seur.element(ww.get.1st.Seur.element)
  recall.genes.ls(recall.genes.ls) --> ww.get.1st.Seur.element(ww.get.1st.Seur.element)
  recall.all.genes(recall.all.genes) --> ww.get.1st.Seur.element(ww.get.1st.Seur.element)
  qQC.plots.BrainOrg(qQC.plots.BrainOrg) --> qUMAP(qUMAP)
  qMarkerCheck.BrainOrg(qMarkerCheck.BrainOrg) --> multiFeaturePlot.A4(multiFeaturePlot.A4)
  ww.check.if.3D.reduction.exist(ww.check.if.3D.reduction.exist) --> RecallReduction(RecallReduction)
  plot.Gene.Cor.Heatmap(plot.Gene.Cor.Heatmap) --> check.genes(check.genes)
  plot.Gene.Cor.Heatmap(plot.Gene.Cor.Heatmap) --> sparse.cor(sparse.cor)
  multiFeatureHeatmap.A4(multiFeatureHeatmap.A4) --> check.genes(check.genes)
  match_best_identity(match_best_identity) --> replace_by_most_frequent_categories(replace_by_most_frequent_categories)
  match_best_identity(match_best_identity) --> clUMAP(clUMAP)
  getClusterNames(getClusterNames) --> GetClusteringRuns(GetClusteringRuns)
  get.clustercomposition(get.clustercomposition) --> clUMAP(clUMAP)
  qUMAP(qUMAP) --> check.genes(check.genes)
  calc.cluster.averages(calc.cluster.averages) --> qUMAP(qUMAP)
  add.meta.fraction(add.meta.fraction) --> check.genes(check.genes)
  SetupReductionsNtoKdimensions(SetupReductionsNtoKdimensions) --> BackupReduction(BackupReduction)
  clUMAP(clUMAP) --> getDiscretePalette(getDiscretePalette)
  clUMAP(clUMAP) --> GetClusteringRuns(GetClusteringRuns)
  RenameClustering(RenameClustering) --> clUMAP(clUMAP)
  PrctCellExpringGene(PrctCellExpringGene) --> ww.calc_helper(ww.calc_helper)
  PrctCellExpringGene(PrctCellExpringGene) --> PrctCellExpringGene(PrctCellExpringGene)
  PlotTopGenesPerCluster(PlotTopGenesPerCluster) --> GetTopMarkers(GetTopMarkers)
  PlotTopGenesPerCluster(PlotTopGenesPerCluster) --> multiFeaturePlot.A4(multiFeaturePlot.A4)
  PlotTopGenes(PlotTopGenes) --> multiFeaturePlot.A4(multiFeaturePlot.A4)
  plot3D.umap.gene(plot3D.umap.gene) --> ww.check.quantile.cutoff.and.clip.outliers(ww.check.quantile.cutoff.and.clip.outliers)
  plot3D.umap.gene(plot3D.umap.gene) --> ww.check.if.3D.reduction.exist(ww.check.if.3D.reduction.exist)
  plot3D.umap.gene(plot3D.umap.gene) --> SavePlotlyAsHtml(SavePlotlyAsHtml)
  plot3D.umap.gene(plot3D.umap.gene) --> Annotate4Plotly3D(Annotate4Plotly3D)
  Plot3D.ListOfGenes(Plot3D.ListOfGenes) --> plot3D.umap.gene(plot3D.umap.gene)
  plot3D.umap(plot3D.umap) --> ww.check.if.3D.reduction.exist(ww.check.if.3D.reduction.exist)
  plot3D.umap(plot3D.umap) --> gg_color_hue(gg_color_hue)
  plot3D.umap(plot3D.umap) --> SavePlotlyAsHtml(SavePlotlyAsHtml)
  plot3D.umap(plot3D.umap) --> Annotate4Plotly3D(Annotate4Plotly3D)
  Plot3D.ListOfCategories(Plot3D.ListOfCategories) --> plot3D.umap(plot3D.umap)
  GetNumberOfClusters(GetNumberOfClusters) --> GetClusteringRuns(GetClusteringRuns)
  GetNamedClusteringRuns(GetNamedClusteringRuns) --> GetClusteringRuns(GetClusteringRuns)
  Downsample.Seurat.Objects.PC(Downsample.Seurat.Objects.PC) --> subsetSeuObj(subsetSeuObj)
  Downsample.Seurat.Objects.PC(Downsample.Seurat.Objects.PC) --> isave.RDS(isave.RDS)
  subsetSeuObj(subsetSeuObj) --> sampleNpc(sampleNpc)
  isave.RDS(isave.RDS) --> .saveRDS.compress.in.BG(.saveRDS.compress.in.BG)
  Downsample.Seurat.Objects(Downsample.Seurat.Objects) --> subsetSeuObj(subsetSeuObj)
  Downsample.Seurat.Objects(Downsample.Seurat.Objects) --> isave.RDS(isave.RDS)
  CalculateFractionInTrome(CalculateFractionInTrome) --> check.genes(check.genes)
  Calc.Cor.Seurat(Calc.Cor.Seurat) --> sparse.cor(sparse.cor)
  BulkGEScatterPlot(BulkGEScatterPlot) --> qqSaveGridA4(qqSaveGridA4)
  multiFeaturePlot.A4(multiFeaturePlot.A4) --> check.genes(check.genes)
  AutoLabelTop.logFC(AutoLabelTop.logFC) --> multiFeaturePlot.A4(multiFeaturePlot.A4)
  AutoLabelTop.logFC(AutoLabelTop.logFC) --> GetTopMarkersDF(GetTopMarkersDF)
  AutoLabel.KnownMarkers(AutoLabel.KnownMarkers) --> GetTopMarkersDF(GetTopMarkersDF)
  Add.DE.combined.score(Add.DE.combined.score) --> SmallestNonAboveX(SmallestNonAboveX)

subgraph Jaccard toolkit
  jPairwiseJaccardIndexList(jPairwiseJaccardIndexList) --> jJaccardIndexVec(jJaccardIndexVec)
  jPairwiseJaccardIndex(jPairwiseJaccardIndex) --> jJaccardIndexBinary(jJaccardIndexBinary)
end

subgraph Gene Update
  ConvertDropSeqfolders(ConvertDropSeqfolders) --> UpdateGenesSeurat(UpdateGenesSeurat)
  Convert10Xfolders.old(Convert10Xfolders.old) --> UpdateGenesSeurat(UpdateGenesSeurat)
  UpdateGenesSeurat(UpdateGenesSeurat) --> RenameGenesSeurat(RenameGenesSeurat)
  UpdateGenesSeurat(UpdateGenesSeurat) --> HGNC.EnforceUnique(HGNC.EnforceUnique)
  UpdateGenesSeurat(UpdateGenesSeurat) --> GetUpdateStats(GetUpdateStats)
  Convert10Xfolders(Convert10Xfolders) --> UpdateGenesSeurat(UpdateGenesSeurat)

end
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