Spatial Projection of Network Signals along Geodesic Paths

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Documentation for package ‘PathwaySpace’ version 1.4.1

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

Help Pages

activeFeature	Accessor Functions for PathwaySpace Objects
activeFeature-method	Accessor Functions for PathwaySpace Objects
activeFeature<-	Accessor Functions for PathwaySpace Objects
activeFeature<--method	Accessor Functions for PathwaySpace Objects
annotation_pspace_signal	Annotation Functions for PathwaySpace Plots
buildPathwaySpace	Constructor of PathwaySpace-class Objects
CGC_20211118	COSMIC-CGC genes mapped to PathwaySpace images
circularProjection	Circular Projection of Graph-Associated Signals
circularProjection-method	Circular Projection of Graph-Associated Signals
expDecay	Constructor of exponential decay functions
gdist.toy	A pruned and laid out igraph object from Pathway Commons V12
getNearestNode	getNearestNode
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	Constructor of linear decay functions
pathDistances	Calculate a pathway space distance between two vectors
PathwaySpace-accessors	Accessor Functions for PathwaySpace Objects
PathwaySpace-class	PathwaySpace: An S4 class for signal projection 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
polarDecay	Polar transformation functions
polarProjection	Polar Projection of Graph-Associated Signals
polarProjection-method	Polar Projection of Graph-Associated Signals
pspace.cols	A simple vector of colors for PathwaySpace images
pspace.pals	Create interpolated color palettes for PathwaySpace images
signalAggregation	Signal aggregation functions
silhouetteMapping	Decorating PathwaySpace Images with Graph Silhouettes
silhouetteMapping-method	Decorating PathwaySpace Images with Graph Silhouettes
SpaceProjection-class	Projection Data Container for PathwaySpace Objects
summitMapping	Mapping Summits on PathwaySpace Images
summitMapping-method	Mapping Summits on PathwaySpace Images
summitWatershed	Variation of the watershed algorithm for summit detection
updatePathwaySpace	Update a PathwaySpace object
updatePathwaySpace-method	Update a PathwaySpace object
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-accessors	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	Constructor of Weibull decay functions