# Spatial Projection of Network Signals along Geodesic Paths

## Documentation for package ‘PathwaySpace’ version 1.0.1

- 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.