Merge pull request #184 from deleip/master

improved visualizeDependencies

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '7183116'
+ValidationKey: '7208614'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9019
+    rev: v0.3.2.9021
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'madrat: May All Data be Reproducible and Transparent (MADRaT) *'
-version: 3.6.6
-date-released: '2023-09-26'
+version: 3.6.7
+date-released: '2023-10-12'
 abstract: Provides a framework which should improve reproducibility and transparency
   in data processing. It provides functionality such as automatic meta data creation
   and management, rudimentary quality management, data caching, work-flow management

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: madrat
 Title: May All Data be Reproducible and Transparent (MADRaT) *
-Version: 3.6.6
-Date: 2023-09-26
+Version: 3.6.7
+Date: 2023-10-12
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "dietrich@pik-potsdam.de", role = c("aut", "cre")),
     person("Lavinia", "Baumstark", , "lavinia@pik-potsdam.de", role = "aut"),

R/visualizeDependencies.R

@@ -132,37 +132,45 @@ visualizeDependencies <- function(..., direction = "both", order = 2, filter = N
     V(fullGraph)$shape <- "circle"
   }
 
+  # make central vertices circles
+  V(fullGraph)$shape[V(fullGraph)$name %in% functions] <- "circle"
 
   # add corresponding mr package to each vertex of graph
   for (i in seq_along(V(fullGraph))) {
     V(fullGraph)$color[i] <- ifelse(V(fullGraph)$name[i] %in% dfGraphMadrat$from,
                                     dfGraphMadrat$from_package[which(dfGraphMadrat$from == V(fullGraph)$name[i])[1]],
                                     dfGraphMadrat$to_package[which(dfGraphMadrat$to == V(fullGraph)$name[i])[1]])
+    V(fullGraph)$frame.color[i] <- V(fullGraph)$color[i]
+    V(fullGraph)$frame.width[i] <- 1
   }
 
   # all packages that are relevant
   pkg <- unique(V(fullGraph)$color)
 
   # set default colors
-  colorsIn <- c("deepskyblue", "gold", "mediumpurple", "#33cbb9", "#219421")
+  colorsVertices <- c("deepskyblue", "gold", "mediumpurple", "#33cba8", "#219421",
+                      "#ff7700", "#d52580", "#3b3bab", "#237791", "#a61818", "#8cdb7d")
 
-  # set vertex colors according to package (different shades for incoming/outgoing)
+  # set vertex colors according to packages
   for (i in seq_along(pkg)) {
-    V(fullGraph)$color[which(V(fullGraph)$color == pkg[i])] <- colorsIn[i]
+    V(fullGraph)$color[which(V(fullGraph)$color == pkg[i])] <- colorsVertices[i]
+    V(fullGraph)$frame.color[which(V(fullGraph)$frame.color == pkg[i])] <- colorsVertices[i]
   }
 
-  # make central vertices red
-  V(fullGraph)$color[V(fullGraph)$name %in% functions] <- "#f84141"
-  V(fullGraph)$shape[V(fullGraph)$name %in% functions] <- "sphere"
+  # for non-central vetices only frame colored
+  V(fullGraph)$color[!(V(fullGraph)$name %in% functions)] <- "white"
+  V(fullGraph)$frame.width[!(V(fullGraph)$name %in% functions)] <- 3
 
   # plot graph
   if (!is.null(filename)) grDevices::png(filename, 800, 800)
   plot(fullGraph)
-  graphics::legend("topright", legend = c(pkg, "Central functions"), pch = 16,
-                   col = c(colorsIn[seq_along(pkg)], "#c93535"), bty = "n")
-  if (direction == "both") graphics::legend("bottomright", legend = c("In", "Out"), pch = c(22, 21), bty = "n")
-  if (direction == "in") graphics::legend("bottomright", legend = c("In"), pch = 22, bty = "n")
-  if (direction == "out") graphics::legend("bottomright", legend = c("Out"), pch = 21, bty = "n")
+  graphics::legend("topright", legend = pkg, pch = 16, col = colorsVertices[seq_along(pkg)], bty = "n")
+  if (direction == "both") graphics::legend("bottomright", legend = c("Central functions", "In", "Out"),
+                                            pch = c(16, 22, 21), bty = "n")
+  if (direction == "in") graphics::legend("bottomright", legend = c("Central functions", "In"),
+                                          pch = c(16, 22), bty = "n")
+  if (direction == "out") graphics::legend("bottomright", legend = c("Central functions", "Out"),
+                                           pch = c(16, 21), bty = "n")
   if (!is.null(filename)) grDevices::dev.off()
 
   # return graph and list of relevant packages

README.md

@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **3.6.6**
+R package **madrat**, version **3.6.7**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/madrat)](https://cran.r-project.org/package=madrat) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1115490.svg)](https://doi.org/10.5281/zenodo.1115490) [![R build status](https://github.com/pik-piam/madrat/workflows/check/badge.svg)](https://github.com/pik-piam/madrat/actions) [![codecov](https://codecov.io/gh/pik-piam/madrat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/madrat) [![r-universe](https://pik-piam.r-universe.dev/badges/madrat)](https://pik-piam.r-universe.dev/builds)
 
@@ -55,7 +55,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **madrat** in publications use:
 
-Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Führlich P (2023). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.6.6, <https://github.com/pik-piam/madrat>.
+Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Führlich P (2023). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi: 10.5281/zenodo.1115490 (URL: https://doi.org/10.5281/zenodo.1115490), R package version 3.6.7, <URL: https://github.com/pik-piam/madrat>.
 
 A BibTeX entry for LaTeX users is
 
@@ -64,7 +64,7 @@ A BibTeX entry for LaTeX users is
   title = {madrat: May All Data be Reproducible and Transparent (MADRaT)},
   author = {Jan Philipp Dietrich and Lavinia Baumstark and Stephen Wirth and Anastasis Giannousakis and Renato Rodrigues and Benjamin Leon Bodirsky and Debbora Leip and Ulrich Kreidenweis and David Klein and Pascal Führlich},
   year = {2023},
-  note = {R package version 3.6.6},
+  note = {R package version 3.6.7},
   doi = {10.5281/zenodo.1115490},
   url = {https://github.com/pik-piam/madrat},
 }