Man pages for davnovak/SingleBench
Framework for benchmarking and optimising dimension-reduction and clustering pipelines in expression data analysis
| AddLayout | Add 2-dimensional layout to a Benchmark object |
| Benchmark | 'Benchmark' object constructor |
| CloneFrom | Clone projection step from some other subpipeline |
| ComputekNNMatrix | Compute a 'k'-nearest-neighbour matrix for expression data |
| CreatePenaltyScoringMatrix | Create a match/mismatch scoring matrix with hierarchical... |
| Evaluate | Evaluate (run) a benchmark |
| ExtendGates | Extend gating to unassigned cells |
| Fix | Fix parameters for a tool wrapper |
| GetAnnotation | Get 'Benchmark' manual annotation |
| GetAnnotationScoring | Get 'Benchmark' manual annotation scoring |
| GetBootstrapIndices | Get 'Benchmark' bootstrap indices |
| GetChannelsAndMarkers | Extract channel and marker names from a collection of FCS... |
| GetClustering | Get 'Benchmark' clustering result |
| GetClusteringInput | Get 'Benchmark' clustering input |
| GetClusteringScores | Get 'Benchmark' clustering evaluation scores |
| GetClusteringScoringTable | Get 'Benchmark' clustering evaluation scores table |
| GetCoRanking | Get 'Benchmark' collapsed co-ranking matrix |
| GetDistanceMatrix | Get 'Benchmark' expression data distance matrix |
| GetExpressionMatrix | Get 'Benchmark' expression data |
| GetkNNMatrix | Get 'Benchmark' expression data 'k'-NN matrix |
| GetLayout | Get 'Benchmark' 2-dimensional layout of input data |
| GetNParameterIterationName | Get 'Benchmark' _n_-parameter iteration name |
| GetNParameterIterationName_Clustering | Get 'Benchmark' _n_-parameter iteration clustering name |
| GetNParameterIterationName_Projection | Get 'Benchmark' _n_-parameter iteration name for a projection... |
| GetNParameterIterationsCount | Get 'Benchmark' _n_-parameter count for subpipeline |
| GetNParameterNames | Get 'Benchmark' _n_-parameter iteration names of a... |
| GetNParameterValues | Get 'Benchmark' _n_-parameter values for a subpipeline |
| GetPenaltyScoringMatrix | Get 'Benchmark' penalty scoring matrix |
| GetProjection | Get 'Benchmark' latent-space projection |
| GetProjectionScores | Get 'Benchmark' dimension-reduction evaluation scores |
| GetProjectionScoringTable | Get 'Benchmark' projection evaluation scores table |
| GetRMSDPerCluster | Get RMSDs of each cluster in clustering result of an... |
| GetScores | Get 'Benchmark' evaluation scores of an _n_-parameter... |
| GetSubpipelineName | Get 'Benchmark' sub-pipeline name |
| Jacc | Match clusters across two clusterings and plot results |
| kNNGTweak | Tweak format of a 'k'-nearest-neighbour graph object |
| LoadWrappers | Load projection and clustering tool wrappers |
| Module | Specify _n_-parameter for a tool wrapper |
| PlotClusterHeatmap | Create a heatmap of expression value medians per cluster |
| PlotClustersOverlay | Create a clusters-overlay plot |
| PlotCompositionMap | Create cluster composition map |
| PlotCoRanking | Plot collapsed co-ranking matrix for heatmap for projection... |
| PlotLabelsOverlay | Create a labels-overlay plot |
| PlotNParameterMap_Clustering | Plot an _n_-parameter map for clustering |
| PlotPopulationHeatmap | Create a heatmap of expression value medians per population |
| PlotRMSDToSize | Plot RMSD-to-size plots for clustering result |
| PlotSimilarityHeatmap | Create a comprehensive similarity heatmap plot |
| ScoreAnnotation | Apply unsupervised evaluation metrics to score manual... |
| ScoreClustering | Normalised Mutual Information' = nmi Normalised Mutual... |
| ShowReadout_Clustering | View readout of clustering evaluation metric values |
| ShowReadout_Projection | View readout of projection evaluation metric values |
| Subpipeline | Create subpipeline of a pipeline |
| WhatIs | Inspect a specific cluster or annotated population |
| WrapTool | Generate a projection or clustering tool wrapper |
