# Spatial Projection of Network Signals along Geodesic Paths

## 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