| 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 |