Spatial Projection of Network Signals along Geodesic Paths

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Documentation for package ‘PathwaySpace’ version 0.99.4

• 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	Creating 2D-landscape images from graph objects.
circularProjection-method	Creating 2D-landscape images from graph objects.
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.
gtoy1	Toy 'igraph' objects.
gtoy2	Toy 'igraph' objects.
gtoys	Toy 'igraph' objects.
hallmarks	A list with Hallmark gene sets (v2023.1).
Hallmarks_v2023_1_Hs_symbols	A list with Hallmark gene sets (v2023.1).
length	Accessor function for PathwaySpace objects.
length-method	Accessor function for PathwaySpace objects.
linearDecay	A simple linear decay function.
names	Accessor functions for PathwaySpace objects.
names-method	Accessor functions for PathwaySpace objects.
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	Creating 2D-landscape images from graph objects.
polarProjection-method	Creating 2D-landscape images from graph objects.
pspace.cols	A simple vector of colors for PathwaySpace images.
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.
vertexSignal	Accessor functions for fetching slots from a PathwaySpace object.
vertexSignal-method	Accessor functions for fetching slots from a PathwaySpace object.
vertexSignal<-	Accessor functions for fetching slots from a PathwaySpace object.
vertexSignal<--method	Accessor functions for fetching slots from a PathwaySpace object.
vertexWeight	Accessor functions for fetching slots from a PathwaySpace object.
vertexWeight-method	Accessor functions for fetching slots from a PathwaySpace object.
vertexWeight<-	Accessor functions for fetching slots from a PathwaySpace object.
vertexWeight<--method	Accessor functions for fetching slots from a PathwaySpace object.
weibullDecay	Weibull decay function.