Package: PathwaySpace 0.99.3

Mauro Castro

PathwaySpace: Spatial Projection of Network Signals along Geodesic Paths

For a given graph containing vertices, edges, and a signal associated with the vertices, the PathwaySpace package performs a convolution operation, which involves a weighted combination of neighboring vertices and their associated signals. The package then uses a decay function to project these signals, creating geodesic paths on a 2D-image space. *PathwaySpace* could have various applications, such as visualizing and analyzing network data in a graphical format that highlights the relationships and signal strengths between vertices. It can be particularly useful for understanding the influence of signals through complex networks. By combining graph theory, signal processing, and visualization, the *PathwaySpace* package provides a novel way of representing and analyzing graph data.

Authors:Vinicius Chagas [ctr], Victor Apolonio [ctr], Mauro Castro [aut, cre]

PathwaySpace_0.99.3.tar.gz
PathwaySpace_0.99.3.zip(r-4.5)PathwaySpace_0.99.3.zip(r-4.4)
PathwaySpace_0.99.3.tgz(r-4.4-any)
PathwaySpace_0.99.3.tar.gz(r-4.5-noble)PathwaySpace_0.99.3.tar.gz(r-4.4-noble)
PathwaySpace_0.99.3.tgz(r-4.4-emscripten)
PathwaySpace.pdf |PathwaySpace.html
PathwaySpace/json (API)
NEWS

# Install 'PathwaySpace' in R:
install.packages('PathwaySpace', repos = c('https://sysbiolab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/sysbiolab/pathwayspace/issues

Datasets:
  • CGC_20211118 - COSMIC-CGC genes mapped to PathwaySpace images.
  • PCv12_pruned_igraph - A pruned and laid out igraph object from Pathway Commons V12.
  • gdist.toy - A pruned and laid out igraph object from Pathway Commons V12.
  • gimage - An image matrix.
  • gtoy1 - Toy 'igraph' objects.
  • gtoy2 - Toy 'igraph' objects.
  • hallmarks - A list with Hallmark gene sets (v2023.1).

On CRAN:

bioinformaticsbiological-networksgraph

4.48 score 1 stars 4 scripts 75 downloads 18 exports 34 dependencies

Last updated 3 months agofrom:8011a2a7b4. Checks:OK: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-winOKNov 04 2024
R-4.5-linuxOKNov 04 2024
R-4.4-winOKNov 04 2024
R-4.4-macOKNov 04 2024

Exports:buildPathwaySpacecircularProjectionexpDecaygetPathwaySpacelinearDecaypathDistancesplotPathDistancesplotPathwaySpacepolarProjectionpspace.colssilhouetteMappingsummitMappingsummitWatershedvertexSignalvertexSignal<-vertexWeightvertexWeight<-weibullDecay

Dependencies:clicolorspacecpp11fansifarverggplot2ggrepelgluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RANNRColorBrewerRcppRGraphSpacerlangscalestibbleutf8vctrsviridisLitewithr

PathwaySpace: Spatial projection of network signals along geodesic paths.

Rendered fromPathwaySpace.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-08-06
Started: 2023-09-29

Readme and manuals

Help Manual

Help pageTopics
Constructor of PathwaySpace-class objects.buildPathwaySpace
COSMIC-CGC genes mapped to PathwaySpace images.CGC_20211118
Creating 2D-landscape images from graph objects.circularProjection circularProjection,PathwaySpace-method
Exponential decay function.expDecay
Accessors for fetching slots from a PathwaySpace object.getPathwaySpace getPathwaySpace,PathwaySpace-method
An image matrix.gimage
Toy 'igraph' objects.gtoy1 gtoy2 gtoys
A list with Hallmark gene sets (v2023.1).hallmarks Hallmarks_v2023_1_Hs_symbols
Accessor function for PathwaySpace objects.length length,PathwaySpace-method
A simple linear decay function.linearDecay
Accessor functions for PathwaySpace objects.names names,PathwaySpace-method
Calculate a pathway space distance between two vectors.pathDistances
PathwaySpace: An S4 class for signal propagation on image spaces.PathwaySpace-class
A pruned and laid out igraph object from Pathway Commons V12.gdist.toy PCv12_pruned_igraph
Accessory function to plot pathway space distances.plotPathDistances
Plotting 2D-landscape images for the PathwaySpace package.plotPathwaySpace plotPathwaySpace,PathwaySpace-method
Creating 2D-landscape images from graph objects.polarProjection polarProjection,PathwaySpace-method
A simple vector of colors for PathwaySpace images.pspace.cols
Decorating PathwaySpace images with graph silhouettes.silhouetteMapping silhouetteMapping,PathwaySpace-method
Mapping summits on PathwaySpace images.summitMapping summitMapping,PathwaySpace-method
Variation of the watershed algorithm for summit detection.summitWatershed
Accessor functions for fetching slots from a PathwaySpace object.vertexSignal vertexSignal,PathwaySpace-method vertexSignal<- vertexSignal<-,PathwaySpace-method
Accessor functions for fetching slots from a PathwaySpace object.vertexWeight vertexWeight,PathwaySpace-method vertexWeight<- vertexWeight<-,PathwaySpace-method
Weibull decay function.weibullDecay