Package index • mfishtools

All functions
`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
`getTopMatch()`	Get top leaf match
`get_subtree_label()`	Gets subtree labels for lca function.
`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-package` `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
`rowMedians()`	Calculate row medians
`smartLayerAllocation()`	Layer weights per cell
`subsampleCells()`	Subsample cells
`summarizeMatrix()`	Summarize matrix
`update_mfishtools()`	Update the mfishtools library

Reference

All functions