Package index • PathwaySpace

PathwaySpace

PathwaySpace-class: PathwaySpace: An S4 class for signal projection on image spaces
buildPathwaySpace(): Constructor of PathwaySpace-class Objects
getPathwaySpace(<PathwaySpace>): Accessors for Fetching Slots from a PathwaySpace Object
updatePathwaySpace(<PathwaySpace>): Update a PathwaySpace object

Accessors

`gs_vertex_attr<-`(<PathwaySpace>) `gs_edge_attr<-`(<PathwaySpace>): Accessor Functions for PathwaySpace Objects
vertexSignal(<PathwaySpace>) `vertexSignal<-`(<PathwaySpace>) vertexDecay(<PathwaySpace>) `vertexDecay<-`(<PathwaySpace>) activeFeature(<PathwaySpace>) `activeFeature<-`(<PathwaySpace>): Accessor Functions for PathwaySpace Objects

Projections

Spatial projection methods and the SpaceProjection class

SpaceProjection-class: Projection Data Container for PathwaySpace Objects
circularProjection(<PathwaySpace>): Circular Projection of Graph-Associated Signals
polarProjection(<PathwaySpace>): Polar Projection of Graph-Associated Signals

Decorations

silhouetteMapping(<PathwaySpace>): Decorating PathwaySpace Images with Graph Silhouettes
summitMapping(<PathwaySpace>): Mapping Summits on PathwaySpace Images
summitWatershed(): Variation of the watershed algorithm for summit detection

Decay functions

Signal decay models used in spatial projection

linearDecay(): Constructor of linear decay functions
expDecay(): Constructor of exponential decay functions
polarDecay(): Polar transformation functions
weibullDecay(): Constructor of Weibull decay functions

Aggregation functions

signalAggregation(): Signal aggregation functions

Path distances

pathDistances(): Calculate a pathway space distance between two vectors
plotPathDistances(): Accessory function to plot pathway space distances
getNearestNode(): getNearestNode

Plotting

plotPathwaySpace(<PathwaySpace>): Plotting 2D-landscape images for the PathwaySpace package
annotation_pspace_signal(): Annotation Functions for PathwaySpace Plots

Utilities

pspace.cols(): A simple vector of colors for PathwaySpace images
pspace.pals(): Create interpolated color palettes for PathwaySpace images
gimage: An image matrix

Data

CGC_20211118: COSMIC-CGC genes mapped to PathwaySpace images
Hallmarks_v2023_1_Hs_symbols: A list with Hallmark gene sets (v2023.1)
PCv12_pruned_igraph: A pruned and laid out igraph object from Pathway Commons V12

Package

PathwaySpace PathwaySpace-package: PathwaySpace: Spatial Projection of Network Signals along Geodesic Paths