# Spatial Projection of Network Signals along Geodesic Paths

## Documentation for package ‘PathwaySpace’ version 1.5.0

- 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