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Milo()
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The Milo constructor |
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annotateNhoods()
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Add annotations from colData to DA testing results |
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buildFromAdjacency
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Build a graph from an input adjacency matrix |
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buildGraph()
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Build a k-nearest neighbour graph |
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buildNhoodGraph()
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Build an abstracted graph of neighbourhoods for visualization |
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calcNhoodDistance()
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Calculate within neighbourhood distances |
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calcNhoodExpression()
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Average expression within neighbourhoods |
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countCells()
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Count cells in neighbourhoods |
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findNhoodMarkers
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Identify post-hoc neighbourhood marker genes |
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graphSpatialFDR
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Control the spatial FDR |
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makeNhoods()
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Define neighbourhoods on a graph (fast) |
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matrixORMatrix-class
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The Milo container class |
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Milo-methods
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Get and set methods for Milo objects |
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plotDAbeeswarm()
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Visualize DA results as a beeswarm plot |
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plotNhoodExpressionDA()
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Visualize gene expression in neighbourhoods |
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plotNhoodGraph()
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Plot graph of neighbourhood |
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plotNhoodGraphDA()
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Plot Milo results on graph of neighbourhood |
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plotNhoodSizeHist()
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Plot histogram of neighbourhood sizes |
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sim_discrete
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sim_discrete |
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sim_trajectory
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Simulated linear trajectory data |
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testDiffExp
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Perform post-hoc differential gene expression analysis |
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testNhoods
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Perform differential neighbourhood abundance testing |