| 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. |