Spatial Projection of Network Signals along Geodesic Paths

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Documentation for package ‘PathwaySpace’ version 1.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

buildPathwaySpace	Constructor of PathwaySpace-class Objects
CGC_20211118	COSMIC-CGC genes mapped to PathwaySpace images
circularProjection	Spatial Projection of Graph-Associated Signals
circularProjection-method	Spatial Projection of Graph-Associated Signals
expDecay	Exponential decay function
gdist.toy	A pruned and laid out igraph object from Pathway Commons V12
getPathwaySpace	Accessors for Fetching Slots from a PathwaySpace Object
getPathwaySpace-method	Accessors for Fetching Slots from a PathwaySpace Object
gimage	An image matrix
gs_edge_attr<-	Accessor Functions for PathwaySpace Objects
gs_edge_attr<--method	Accessor Functions for PathwaySpace Objects
gs_vertex_attr<-	Accessor Functions for PathwaySpace Objects
gs_vertex_attr<--method	Accessor Functions for PathwaySpace Objects
hallmarks	A list with Hallmark gene sets (v2023.1)
Hallmarks_v2023_1_Hs_symbols	A list with Hallmark gene sets (v2023.1)
linearDecay	A simple linear decay function
pathDistances	Calculate a pathway space distance between two vectors
PathwaySpace-class	PathwaySpace: An S4 class for signal propagation on image spaces
PCv12_pruned_igraph	A pruned and laid out igraph object from Pathway Commons V12
plotPathDistances	Accessory function to plot pathway space distances
plotPathwaySpace	Plotting 2D-landscape images for the PathwaySpace package
plotPathwaySpace-method	Plotting 2D-landscape images for the PathwaySpace package
polarProjection	Spatial Projection of Graph-Associated Signals
polarProjection-method	Spatial Projection of Graph-Associated Signals
pspace.cols	A simple vector of colors for PathwaySpace images
signalAggregation	Signal aggregation functions
signalDecay	Signal decay functions
silhouetteMapping	Decorating PathwaySpace Images with Graph Silhouettes
silhouetteMapping-method	Decorating PathwaySpace Images with Graph Silhouettes
summitMapping	Mapping Summits on PathwaySpace Images
summitMapping-method	Mapping Summits on PathwaySpace Images
summitWatershed	Variation of the watershed algorithm for summit detection
vertexDecay	Accessor Functions for PathwaySpace Objects
vertexDecay-method	Accessor Functions for PathwaySpace Objects
vertexDecay<-	Accessor Functions for PathwaySpace Objects
vertexDecay<--method	Accessor Functions for PathwaySpace Objects
vertexSignal	Accessor Functions for PathwaySpace Objects
vertexSignal-method	Accessor Functions for PathwaySpace Objects
vertexSignal<-	Accessor Functions for PathwaySpace Objects
vertexSignal<--method	Accessor Functions for PathwaySpace Objects
weibullDecay	Weibull decay function