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sysbiolab · Nov 12, 2024 · 77276ca · 77276ca
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,17 +1,17 @@
 Package: PathwaySpace
 Type: Package
 Title: Spatial Projection of Network Signals along Geodesic Paths
-Version: 0.99.3
+Version: 1.0.0
 Authors@R: 
-    c(person("Vinicius", "Chagas", role = "ctr"),
-      person("Victor", "Apolonio", role = "ctr"),
+    c(person("Victor", "Apolonio", role = "ctr"),
+      person("Vinicius", "Chagas", role = "ctr"),
       person("Mauro", "Castro", role = c("aut", "cre"),
               email = "mauro.a.castro@gmail.com",
               comment = c(ORCID = "0000-0003-4942-8131")))
 Depends: R(>= 4.4), methods, RGraphSpace
 Imports: grDevices, stats, scales, igraph, RANN, ggplot2, ggrepel
 Suggests: knitr, rmarkdown, testthat, 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.
+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
 VignetteBuilder: knitr
 URL: https://github.com/sysbiolab/PathwaySpace
@@ -27,4 +27,4 @@ Collate:
     pspaceMethods.R
     pspacePlots.R
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/R/pspaceWatershed.R b/R/pspaceWatershed.R
@@ -33,7 +33,9 @@
 #' # [1] 0 1
 #'
 #' # Check image
-#' # image(gimage)
+#' \donttest{
+#' image(gimage)
+#' }
 #'
 #' # Threshold the signal intensity, for example:
 #' gimage[gimage < 0.5] <- 0
@@ -42,7 +44,9 @@
 #' gmask <- summitWatershed(x = gimage)
 #'
 #' # Check resulting image mask
-#' # image(gmask)
+#' \donttest{
+#' image(gimage)
+#' }
 #'
 #' @aliases summitWatershed
 #' @export

diff --git a/README.md b/README.md
@@ -1,7 +1,10 @@
-### PathwaySpace: Spatial projection of network signals along geodesic paths
+### *PathwaySpace*: Spatial projection of network signals along geodesic paths
   <!-- badges: start -->
-  [![R-CMD-check](https://github.com/sysbiolab/PathwaySpace/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sysbiolab/PathwaySpace/actions/workflows/R-CMD-check.yaml)
-  [![License: Artistic-2.0](https://img.shields.io/badge/license-Artistic--2.0-blue.svg)](https://cran.r-project.org/web/licenses/Artistic-2.0)
+  [![](https://www.r-pkg.org/badges/version/PathwaySpace)](https://cran.r-project.org/package=PathwaySpace)
+  [![](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
+  [![](https://cranlogs.r-pkg.org/badges/PathwaySpace)](https://cran.r-project.org/package=PathwaySpace)
+  [![](https://img.shields.io/badge/license-Artistic--2.0-blue.svg)](https://cran.r-project.org/web/licenses/Artistic-2.0)
+  [![](https://img.shields.io/badge/doi-10.32614/CRAN.package.PathwaySpace-blue.svg)](https://doi.org/10.32614/CRAN.package.PathwaySpace)
   <!-- badges: end -->
 *PathwaySpace* is an R package that creates landscape images from graphs containing vertices (nodes), edges (lines), and a signal associated with the vertices. The package processes the signal using a convolution algorithm that considers the graph's topology to project the signal on a 2D space. 
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -1,9 +1,9 @@
 
 bibentry(bibtype = "Manual",
-author = "'Sysbiolab Team'",
-title = "PathwaySpace: Spatial projection of network signals along geodesic paths.",
+author = person("Sysbiolab Team"),
+title = "PathwaySpace: Spatial projection of network signals along geodesic paths",
 year = "2024",
 note = "R package",
 url = "https://github.com/sysbiolab/PathwaySpace",
 textVersion = "Sysbiolab Team. PathwaySpace: Spatial projection of network signals along geodesic paths. R package, 2024."
-)
+)
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -2,6 +2,12 @@
 \title{PathwaySpace News}
 \encoding{UTF-8}
 
+\section{CHANGES IN VERSION 1.0.0 (2024-11-11)}{
+  \itemize{
+    \item Stable release of PathwaySpace.
+  }
+}
+
 \section{CHANGES IN VERSION 0.99.0 (2023-09-08)}{
   \itemize{
     \item 1st release of PathwaySpace.

diff --git a/man/summitWatershed.Rd b/man/summitWatershed.Rd
diff --git a/vignettes/PathwaySpace.Rmd b/vignettes/PathwaySpace.Rmd
@@ -13,7 +13,7 @@ output:
     toc_depth: 2
     css: custom.css
 vignette: >
-  %\VignetteIndexEntry{"PathwaySpace: signals along geodesic paths."}
+  %\VignetteIndexEntry{"PathwaySpace: signals along geodesic paths"}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---