Milo()

The Milo constructor 
annotateNhoods()

Add annotations from colData to DA testing results 
buildFromAdjacency

Build a graph from an input adjacency matrix 
buildGraph()

Build a knearest neighbour graph 
buildNhoodGraph()

Build an abstracted graph of neighbourhoods for visualization 
calcNhoodDistance()

Calculate within neighbourhood distances 
calcNhoodExpression()

Average expression within neighbourhoods 
countCells()

Count cells in neighbourhoods 
findNhoodMarkers

Identify posthoc neighbourhood marker genes 
graphSpatialFDR

Control the spatial FDR 
makeNhoods()

Define neighbourhoods on a graph (fast) 
matrixORMatrixclass

The Milo container class 
Milomethods

Get and set methods for Milo objects 
plotDAbeeswarm()

Visualize DA results as a beeswarm plot 
plotNhoodExpressionDA()

Visualize gene expression in neighbourhoods 
plotNhoodGraph()

Plot graph of neighbourhood 
plotNhoodGraphDA()

Plot Milo results on graph of neighbourhood 
plotNhoodSizeHist()

Plot histogram of neighbourhood sizes 
sim_discrete

sim_discrete 
sim_trajectory

Simulated linear trajectory data 
testDiffExp

Perform posthoc differential gene expression analysis 
testNhoods

Perform differential neighbourhood abundance testing 