Man pages for AllenInstitute/mfishtools
Building Gene Sets and Mapping mFISH Data
| buildMappingBasedMarkerPanel | Greedy algorithm for building marker gene panel |
| buildPanel_oneCluster | Build panel for one cluster (beta) |
| buildQualityTable | Correct mapping at different tree heights |
| buildTreeFromGenePanel | Build and plot dendrogram from gene panel |
| cellToClusterMapping_byCor | Return top mapped correlation-based cluster and confidence |
| cellToClusterMapping_byRank | Cell-based cluster mapping |
| corTreeMapping | Correlation-based cluster mapping |
| corTreeMapping_withFilter | Correlation between nodes and leafs (deprecated) |
| distTreeMapping | (Euclidean) distance mapping |
| filterByClass | Filter by meta-data |
| filterCells | Filter (subset) fishScaleAndMap object |
| filterPanelGenes | Filter genes for spatial transcriptomics panel |
| fishScaleAndMap | Scale mFISH data and map to RNA-seq reference |
| fractionCorrectPerNode | Fraction of correct calls per node |
| fractionCorrectWithGenes | Fraction of cells correctly assigned |
| generateMultipleCellReferenceSet | Generate reference set of pseudo-cells |
| getBetaScore | Get binary (aka beta) score |
| getBranchList | Branch list |
| getConfusionMatrix | Confusion matrix |
| getDend | Build a dendrogram from gene panel |
| getNodeHeight | Get node height |
| get_subtree_label | Gets subtree labels for lca function. |
| getTopMatch | Get top leaf match |
| labelDend | Label dendrogram nodes |
| layerFraction | Layer weights per cell |
| layerScale | Fraction of cells per layer |
| lca | Get lowest common ancestor (defined cluster pairs) |
| leafToNodeMedians | Return mean node expression |
| makeLCAtable | Get lowest common ancestor (all cluster pairs in tree) |
| map_dend | Tree-based mapping |
| mergeFish | Merge two fishScaleAndMap objects |
| mfishtools | mfishtools: Building Gene Sets and Mapping mFISH Data. |
| outputTopConfused | Table of confused clusters |
| plotConfusionVsConfidence | Confusion plot vs. confidence |
| plotCorrectWithGenes | Plot fraction correct |
| plotDistributions | Plot distributions |
| plotHeatmap | Plot heatmap |
| plotNodes | Plot dendrogram |
| plotTsne | Plot TSNE |
| possibleClustersByPriors | Filter possible cluster calls using priors |
| quantileTruncate | Quantile normalize, truncate, and scale |
| resolve_cl | Tree-based mapping (internal) |
| rfTreeMapping | Tree-based mapping |
| rotateXY | Rotate coordinates |
| smartLayerAllocation | Layer weights per cell |
| subsampleCells | Subsample cells |
| summarizeMatrix | Summarize matrix |
| update_mfishtools | Update the mfishtools library |
