added filter argument in visualizeDependencies

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '6647340'
+ValidationKey: '6845650'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

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: 3.4.0
-date-released: '2023-07-13'
+version: 3.5.0
+date-released: '2023-07-21'
 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: 3.4.0
-Date: 2023-07-13
+Version: 3.5.0
+Date: 2023-07-21
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre")),
     person("Lavinia", "Baumstark", , "[email protected]", role = "aut"),

R/visualizeDependencies.R

@@ -2,25 +2,26 @@
 #'
 #' Creates a graphical visualization of dependencies between functions in the mr-universe.
 #'
-#' @param functions function or vector of functions to be analyzed
+#' @param ... function(s) to be analyzed
 #' @param direction Character string, either “in”, “out” or "both". If “in” all sources
 #' feeding into the function are listed. If “out” consumer of the function are listed.
 #' If “both” the union of "in" and "out" is returned.
 #' @param order order of dependencies. Order 1 would be only functions directly called from (in case
 #' of direction "in") or directly calling (in case of direction "out") are shown. Order 2 will also
 #' show direct dependencies of the order 1 dependencies, order 3 also the direct dependencies from
 #' order 2 dependencies, etc.
+#' @param filter regular expression to describe elements which should be excluded from visualization
+#' (e.g. "^tool" to exclude all tool functions)
 #' @param packages packages to use when searching dependencies
 #' @param filename If a filename is provided, the resulting graph will be saved
-#' @author Debbora Leip
+#' @author Debbora Leip, Jan Philipp Dietrich
 #' @seealso \code{\link{getDependencies}}, \code{\link{getMadratGraph}}, \code{\link{getMadratInfo}}
 #' @importFrom igraph make_ego_graph ego V V<- union
 #' @export
 
 
-visualizeDependencies <- function(functions, direction = "both", order = 2, #nolint
+visualizeDependencies <- function(..., direction = "both", order = 2, filter = NULL, # nolint: cyclocomp_linter
                                   packages = getConfig("packages"), filename = NULL) {
-
   # check for required packages
   if (!requireNamespace("graphics", quietly = TRUE)) {
     stop("Package \`graphics\` required to visualize dependencies")
@@ -29,6 +30,8 @@ visualizeDependencies <- function(functions, direction = "both", order = 2, #nol
     stop("Package \`grDevices\` required to save dependency graph")
   }
 
+  functions <- c(...)
+
   # get next order of neighbors
   nextOrder <- function(graph, nodes, mode) {
     egoGraph <- make_ego_graph(graph, nodes, order = 1, mode = mode)
@@ -40,8 +43,9 @@ visualizeDependencies <- function(functions, direction = "both", order = 2, #nol
   combineGraphs1 <- function(graphs) {
     graph <- graphs[[1]]
     if (length(graphs) > 1) {
-      for (i in 2:length(graphs))
+      for (i in 2:length(graphs)) {
         graph <- igraph::union(graph, graphs[[i]])
+      }
     }
     return(graph)
   }
@@ -61,7 +65,6 @@ visualizeDependencies <- function(functions, direction = "both", order = 2, #nol
 
     # find dependencies up to given order in both directions
     for (func in functions) {
-
       # direct neighbors incoming
       current <- nextOrder(graphMadrat, func, mode)
       graphTmp <- current[[1]][[1]]
@@ -87,6 +90,18 @@ visualizeDependencies <- function(functions, direction = "both", order = 2, #nol
 
   # get full graph
   dfGraphMadrat <- getMadratGraph(packages = packages)
+
+  if (!is.null(filter)) {
+    # exclude all entries which match the filter, but exclude target functions
+    # from filter
+    .filter <- function(x, filter, f) {
+      functionFilter <- paste0("^(", paste(f, collapse = "|"), ")$")
+      return(!grepl(filter, x) | grepl(functionFilter, x))
+    }
+    dfGraphMadrat <- dfGraphMadrat[.filter(dfGraphMadrat$to, filter, functions) &
+                                     .filter(dfGraphMadrat$from, filter, functions), ]
+  }
+
   graphMadrat <- graph_from_data_frame(dfGraphMadrat)
 
   # functions as list
@@ -121,8 +136,8 @@ visualizeDependencies <- function(functions, direction = "both", order = 2, #nol
   # 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)$name[i])[1]])
+                                    dfGraphMadrat$from_package[which(dfGraphMadrat$from == V(fullGraph)$name[i])[1]],
+                                    dfGraphMadrat$to_package[which(dfGraphMadrat$to == V(fullGraph)$name[i])[1]])
   }
 
   # all packages that are relevant
@@ -144,7 +159,7 @@ visualizeDependencies <- function(functions, direction = "both", order = 2, #nol
   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")
+                   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")

README.md

@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **3.4.0**
+R package **madrat**, version **3.5.0**
 
 [![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 (URL: https://doi.org/10.5281/zenodo.1115490), R package version 3.4.0, <URL: 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 3.5.0, <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 3.4.0},
+  note = {R package version 3.5.0},
   doi = {10.5281/zenodo.1115490},
   url = {https://github.com/pik-piam/madrat},
 }