Merge branch 'main' into feat/github-workflow-build-doc

.gitignore

@@ -1,4 +1,3 @@
-.Rproj.user
 .Rhistory
 .RData
 .Ruserdata
@@ -8,3 +7,4 @@ renv
 /Meta/
 .DS_Store
 doc
+.Rproj.user

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: PathwaySpace
 Type: Package
 Title: Spatial projection of network signals along geodesic paths
-Version: 0.99.6
+Version: 0.99.0
 Authors@R: 
     c(person("Vinicius", "Chagas", role = "ctr"),
       person("Victor", "Apolonio", role = "ctr"),
       person("Mauro", "Castro", role = c("aut", "cre"),
               email = "mauro.a.castro@gmail.com",
               comment = c(ORCID = "0000-0003-4942-8131")))
-Depends: R(>= 4.2), methods
-Imports: grDevices, stats, scales, igraph, RANN, ggplot2, ggrepel, ggforce, grid
+Depends: R(>= 4.2), methods, RGraphSpace
+Imports: grDevices, stats, scales, igraph, RANN, ggplot2, ggrepel
 Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle, RedeR
 Description: 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.
 License: Artistic-2.0
@@ -25,7 +25,6 @@ Collate:
     pspaceClasses.R
     pspaceGenerics.R
     pspaceMethods.R
-    pspaceImage.R
-    pspaceGraph.R
+    pspacePlots.R
 Encoding: UTF-8
 RoxygenNote: 7.2.3

NAMESPACE

@@ -13,16 +13,15 @@ exportMethods(circularProjection)
 exportMethods(getPathwaySpace)
 exportMethods(length)
 exportMethods(names)
-exportMethods(plotGraphSpace)
-exportMethods(plotImageSpace)
+exportMethods(plotPathwaySpace)
 exportMethods(polarProjection)
 exportMethods(silhouetteMapping)
 exportMethods(summitMapping)
 exportMethods(vertexSignal)
 exportMethods(vertexWeight)
 import(methods)
 importFrom(RANN,nn2)
-importFrom(ggforce,geom_circle)
+importFrom(RGraphSpace,plotGraphSpace)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,annotate)
 importFrom(ggplot2,coord_fixed)
@@ -31,9 +30,7 @@ importFrom(ggplot2,element_line)
 importFrom(ggplot2,element_rect)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,expansion)
-importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_raster)
-importFrom(ggplot2,geom_segment)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,margin)
 importFrom(ggplot2,scale_fill_gradientn)
@@ -48,8 +45,6 @@ importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,convertColor)
 importFrom(grDevices,rgb)
-importFrom(grid,arrow)
-importFrom(grid,unit)
 importFrom(igraph,'E<-')
 importFrom(igraph,'V<-')
 importFrom(igraph,E)

R/pspaceClasses.R

@@ -18,8 +18,7 @@
 #' @method silhouetteMapping \code{\link{silhouetteMapping}}
 #' @method summitMapping \code{\link{summitMapping}}
 #' @method getPathwaySpace \code{\link{getPathwaySpace}}
-#' @method plotImageSpace \code{\link{plotImageSpace}}
-#' @method plotGraphSpace \code{\link{plotGraphSpace}}
+#' @method plotPathwaySpace \code{\link{plotPathwaySpace}}
 #' @aliases PathwaySpace-class
 #' @return An S4 class object.
 #' @section Constructor:

R/pspaceGenerics.R

@@ -27,7 +27,7 @@ setGeneric("summitMapping",
     }, package = "PathwaySpace"
 )
 
-setGeneric("plotImageSpace", 
+setGeneric("plotPathwaySpace", 
     function(pts, colors = pspace.cols(), trim.colors = c(3, 2, 1, 2, 3), 
         bg.color = "grey85", theme.name = c("th0", "th1", "th2", "th3"),
         title = "PathwaySpace", font.size = 1, font.color = "white",
@@ -36,17 +36,7 @@ setGeneric("plotImageSpace",
         add.contour = TRUE, contour.color = "white", marks = FALSE, 
         mark.size = 3, mark.color = "white", mark.padding = 0.5, 
         mark.line.width = 0.5, use.dotmark = FALSE) {
-        standardGeneric("plotImageSpace")
-    }, package = "PathwaySpace"
-)
-
-setGeneric("plotGraphSpace", 
-    function(pts, node.size = 1, edge.width = 0.5, 
-        node.color = "grey50", edge.color = "grey80", bg.color = "grey95",
-        font.size = 1, theme.name = c("th0", "th1", "th2", "th3"),
-        xlab = "Pathway coordinates 1", ylab = "Pathway coordinates 2",
-        marks = FALSE, mark.size = 3, mark.color = "grey20") {
-        standardGeneric("plotGraphSpace")
+        standardGeneric("plotPathwaySpace")
     }, package = "PathwaySpace"
 )
 

R/pspaceMisc.R

@@ -37,7 +37,7 @@
 #' \tab Mapping summits on a 2D-landscape image.\cr
 #' \link{getPathwaySpace}: 
 #' \tab Accessory method for fetching slots from a PathwaySpace object.\cr
-#' \link{plotImageSpace}: 
+#' \link{plotPathwaySpace}: 
 #' \tab Plotting 2D-landscape images for the PathwaySpace package.\cr
 #' }
 #' Further information is available in the vignettes by typing
@@ -213,7 +213,7 @@ NULL
 #'
 #' @param n Number of colors.
 #' @return A vector with hexadecimal color codes.
-#' @seealso \code{\link{plotImageSpace}}
+#' @seealso \code{\link{plotPathwaySpace}}
 #' @examples
 #' pspace.cols()
 #'

R/pspaceImage.R → R/pspacePlots.R

@@ -1,6 +1,6 @@
 #' @title Plotting 2D-landscape images for the PathwaySpace package.
 #'
-#' @description \code{plotImageSpace} is a wrapper function to 
+#' @description \code{plotPathwaySpace} is a wrapper function to 
 #' create dedicated ggplot graphics for PathwaySpace-class objects.
 #'
 #' @param pts A \linkS4class{PathwaySpace} class object.
@@ -67,7 +67,7 @@
 #' pts <- silhouetteMapping(pts)
 #'
 #' # Plot a 2D-landscape image
-#' plotImageSpace(pts)
+#' plotPathwaySpace(pts)
 #' 
 #' @import methods
 #' @docType methods
@@ -79,11 +79,12 @@
 #' @importFrom ggrepel geom_text_repel
 #' @importFrom grDevices convertColor col2rgb rgb
 #' @importFrom grDevices adjustcolor colorRampPalette
-#' @rdname plotImageSpace-methods
-#' @aliases plotImageSpace
+#' @importFrom RGraphSpace plotGraphSpace
+#' @rdname plotPathwaySpace-methods
+#' @aliases plotPathwaySpace
 #' @export
 #'
-setMethod("plotImageSpace", "PathwaySpace", 
+setMethod("plotPathwaySpace", "PathwaySpace", 
     function(pts, colors = pspace.cols(), trim.colors = c(3, 2, 1, 2, 3), 
         bg.color = "grey85", theme.name = c("th0", "th1", "th2", "th3"),
         title = "PathwaySpace", font.size = 1, font.color = "white",

README.md

@@ -19,6 +19,7 @@ BiocManager::install("BiocStyle")
 
 ```r
 install.packages("remotes")
+remotes::install_github("sysbiolab/RGraphSpace", build_vignettes=TRUE)
 remotes::install_github("sysbiolab/PathwaySpace", build_vignettes=TRUE)
 ```