fixed CRAN issues and removed dependencies (#86)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: graphlayouts
 Title: Additional Layout Algorithms for Network Visualizations
-Version: 1.1.1
+Version: 1.1.1.9000
 Authors@R: person("David", "Schoch", email = "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-2952-4812"))
 Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'. 
@@ -13,19 +13,14 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports: 
-    igraph,
+    igraph (>= 2.0.0),
     Rcpp
 Suggests:
-    oaqc,
     testthat,
-    ggraph,
     ggplot2,
-    knitr,
-    rmarkdown,
     uwot
 LinkingTo: 
     Rcpp,
     RcppArmadillo
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
-VignetteBuilder: knitr

NAMESPACE

@@ -34,6 +34,7 @@ export(layout_with_sparse_stress)
 export(layout_with_stress)
 export(layout_with_stress3D)
 export(layout_with_umap)
+export(oaqc)
 export(reorder_edges)
 importFrom(Rcpp,sourceCpp)
 useDynLib(graphlayouts, .registration = TRUE)

NEWS.md

@@ -1,3 +1,10 @@
+# graphlayouts 1.2.0
+
+* ported relevant code from archived R package oaqc (#83)
+* fixed igraph deprecation warnings and require igraph >= 2.0.0 
+* removed vignette and point to tutorial
+* removed dependency of ggraph
+
 # graphlayouts 1.1.1
 
 * fixed bug in disconnected layouts #80

R/annotate_functions.R

@@ -7,47 +7,46 @@
 #' @return concentric circles around origin
 #' @examples
 #' library(igraph)
-#' library(ggraph)
-
-#' g <- sample_gnp(10,0.4)
+#' g <- sample_gnp(10, 0.4)
 #'
 #' \dontrun{
-#' ggraph(g,layout = "centrality",centrality = degree(g))+
-#'   draw_circle(use = "cent")+
-#'   geom_edge_link()+
-#'   geom_node_point(shape = 21,fill = "grey25",size = 5)+
-#'   theme_graph()+
-#'   coord_fixed()
+#' library(ggraph)
+#' ggraph(g, layout = "centrality", centrality = degree(g)) +
+#'     draw_circle(use = "cent") +
+#'     geom_edge_link() +
+#'     geom_node_point(shape = 21, fill = "grey25", size = 5) +
+#'     theme_graph() +
+#'     coord_fixed()
 #' }
 #' @export
 #'
 
 draw_circle <- function(col = "#00BFFF", use = "focus", max.circle) {
-  if (!requireNamespace("ggplot2", quietly = TRUE)) {
-    stop("ggplot2 needed for this function to work. Please install it.", call. = FALSE)
-  }
-  if (!use %in% c("focus", "cent")) {
-    stop("use must be one of 'focus' or 'cent'")
-  }
-  if (use == "focus" && missing(max.circle)) {
-    stop("max.circle missing. Should be set to the max distance from focal node.")
-  }
-  dat <- data.frame()
-  if (use == "cent") {
-    for (d in seq(0, 100, 20) * 2) {
-      tmp <- as.data.frame(circleFun(center = c(0, 0), diameter = d))
-      tmp[["grp"]] <- d
-      dat <- rbind(dat, tmp)
+    if (!requireNamespace("ggplot2", quietly = TRUE)) {
+        stop("ggplot2 needed for this function to work. Please install it.", call. = FALSE)
+    }
+    if (!use %in% c("focus", "cent")) {
+        stop("use must be one of 'focus' or 'cent'")
+    }
+    if (use == "focus" && missing(max.circle)) {
+        stop("max.circle missing. Should be set to the max distance from focal node.")
     }
-  } else if (use == "focus") {
-    for (d in 1:max.circle) {
-      tmp <- as.data.frame(circleFun(center = c(0, 0), diameter = 2 * d))
-      tmp[["grp"]] <- d
-      dat <- rbind(dat, tmp)
+    dat <- data.frame()
+    if (use == "cent") {
+        for (d in seq(0, 100, 20) * 2) {
+            tmp <- as.data.frame(circleFun(center = c(0, 0), diameter = d))
+            tmp[["grp"]] <- d
+            dat <- rbind(dat, tmp)
+        }
+    } else if (use == "focus") {
+        for (d in 1:max.circle) {
+            tmp <- as.data.frame(circleFun(center = c(0, 0), diameter = 2 * d))
+            tmp[["grp"]] <- d
+            dat <- rbind(dat, tmp)
+        }
     }
-  }
-  circs <- ggplot2::geom_path(data = dat, ggplot2::aes_(x = ~x, y = ~y, group = ~grp), col = col, alpha = 0.5)
-  return(circs)
+    circs <- ggplot2::geom_path(data = dat, ggplot2::aes_(x = ~x, y = ~y, group = ~grp), col = col, alpha = 0.5)
+    return(circs)
 }
 
 
@@ -62,62 +61,62 @@ draw_circle <- function(col = "#00BFFF", use = "focus", max.circle) {
 #' @return annotated concentric circles around origin
 #' @examples
 #' library(igraph)
-#' library(ggraph)
 #'
 #' g <- sample_gnp(10, 0.4)
 #' \dontrun{
+#' library(ggraph)
 #' ggraph(g, layout = "centrality", centrality = closeness(g)) +
-#'   draw_circle(use = "cent") +
-#'   annotate_circle(closeness(g), pos = "bottom", format = "scientific") +
-#'   geom_edge_link() +
-#'   geom_node_point(shape = 21, fill = "grey25", size = 5) +
-#'   theme_graph() +
-#'   coord_fixed()
+#'     draw_circle(use = "cent") +
+#'     annotate_circle(closeness(g), pos = "bottom", format = "scientific") +
+#'     geom_edge_link() +
+#'     geom_node_point(shape = 21, fill = "grey25", size = 5) +
+#'     theme_graph() +
+#'     coord_fixed()
 #' }
 #' @export
 #'
 annotate_circle <- function(cent, col = "#00BFFF", format = "", pos = "top", text_size = 3) {
-  if (!requireNamespace("ggplot2", quietly = TRUE)) {
-    stop("ggplot2 needed for this function to work. Please install it.", call. = FALSE)
-  }
-  if (length(cent) == 1) {
-    cent <- seq(1, cent, 1)
-    dat_annot <- data.frame(y = seq(0, 100, 20), x = 0, val = interpolate_cent(cent, seq(0, 100, 20)))
-    dat_annot[["val"]] <- round(dat_annot[["val"]], 8)
-  } else {
-    dat_annot <- data.frame(y = 100 - seq(0, 100, 20), x = 0, val = interpolate_cent(cent, seq(0, 100, 20)))
-    dat_annot[["val"]] <- round(dat_annot[["val"]], 8)
-  }
-  vju <- 0
-  if (format == "scientific") {
-    dat_annot[["val"]] <- format(dat_annot[["val"]], scientific = TRUE)
-  }
-  if (pos == "bottom") {
-    dat_annot[["y"]] <- -dat_annot[["y"]]
-    vju <- 1
-  }
+    if (!requireNamespace("ggplot2", quietly = TRUE)) {
+        stop("ggplot2 needed for this function to work. Please install it.", call. = FALSE)
+    }
+    if (length(cent) == 1) {
+        cent <- seq(1, cent, 1)
+        dat_annot <- data.frame(y = seq(0, 100, 20), x = 0, val = interpolate_cent(cent, seq(0, 100, 20)))
+        dat_annot[["val"]] <- round(dat_annot[["val"]], 8)
+    } else {
+        dat_annot <- data.frame(y = 100 - seq(0, 100, 20), x = 0, val = interpolate_cent(cent, seq(0, 100, 20)))
+        dat_annot[["val"]] <- round(dat_annot[["val"]], 8)
+    }
+    vju <- 0
+    if (format == "scientific") {
+        dat_annot[["val"]] <- format(dat_annot[["val"]], scientific = TRUE)
+    }
+    if (pos == "bottom") {
+        dat_annot[["y"]] <- -dat_annot[["y"]]
+        vju <- 1
+    }
 
-  circs <- ggplot2::geom_text(
-    data = dat_annot, ggplot2::aes_(x = ~x, y = ~y, label = ~val),
-    col = col, vjust = vju, size = text_size
-  )
-  return(circs)
+    circs <- ggplot2::geom_text(
+        data = dat_annot, ggplot2::aes_(x = ~x, y = ~y, label = ~val),
+        col = col, vjust = vju, size = text_size
+    )
+    return(circs)
 }
 
 
 # helper -----
 circleFun <- function(center = c(0, 0), diameter = 1, npoints = 100) {
-  r <- diameter / 2
-  tt <- seq(0, 2 * pi, length.out = npoints)
-  xx <- center[1] + r * cos(tt)
-  yy <- center[2] + r * sin(tt)
-  return(data.frame(x = xx, y = yy))
+    r <- diameter / 2
+    tt <- seq(0, 2 * pi, length.out = npoints)
+    xx <- center[1] + r * cos(tt)
+    yy <- center[2] + r * sin(tt)
+    return(data.frame(x = xx, y = yy))
 }
 
 interpolate_cent <- function(cent, x) {
-  a <- min(cent)
-  b <- max(cent)
-  alpha <- 100 / (b - a)
-  beta <- -100 / (b - a) * a
-  (x - beta) / alpha
+    a <- min(cent)
+    b <- max(cent)
+    alpha <- 100 / (b - a)
+    beta <- -100 / (b - a) * a
+    (x - beta) / alpha
 }

R/graph_manipulate.R

@@ -10,7 +10,6 @@
 #' @return manipulated graph
 #' @examples
 #' library(igraph)
-#' library(ggraph)
 #'
 #' g <- sample_gnp(10, 0.5)
 #' E(g)$attr <- 1:ecount(g)
@@ -24,21 +23,21 @@ NULL
 #' @export
 
 reorder_edges <- function(g, attr, desc = TRUE) {
-  if (!"name" %in% igraph::vertex_attr_names(g)) {
-    igraph::V(g)$name <- 1:igraph::vcount(g)
-  }
-  edges_df <- igraph::as_data_frame(g, what = "edges")
-  edges_df <- edges_df[order(edges_df[[attr]], decreasing = desc), ]
+    if (!"name" %in% igraph::vertex_attr_names(g)) {
+        igraph::V(g)$name <- 1:igraph::vcount(g)
+    }
+    edges_df <- igraph::as_data_frame(g, what = "edges")
+    edges_df <- edges_df[order(edges_df[[attr]], decreasing = desc), ]
 
-  vertices <- igraph::as_data_frame(g, what = "vertices")
-  vattrs <- igraph::vertex_attr_names(g)
-  idname <- which(vattrs == "name")
-  vertices <- vertices[, c(idname, setdiff(seq_along(vattrs), idname))]
+    vertices <- igraph::as_data_frame(g, what = "vertices")
+    vattrs <- igraph::vertex_attr_names(g)
+    idname <- which(vattrs == "name")
+    vertices <- vertices[, c(idname, setdiff(seq_along(vattrs), idname))]
 
-  gn <- igraph::graph_from_data_frame(
-    d = edges_df,
-    directed = igraph::is.directed(g),
-    vertices = vertices
-  )
-  gn
+    gn <- igraph::graph_from_data_frame(
+        d = edges_df,
+        directed = igraph::is_directed(g),
+        vertices = vertices
+    )
+    gn
 }

R/graphlayouts.R

@@ -17,6 +17,6 @@
 #' \item `layout_as_dynamic()` for longitudinal network data
 #' }
 #'
-#' A detailed tutorial can be found at <https://www.mr.schochastics.net/material/netVizR/>
+#' A detailed tutorial can be found at <https://schochastics.github.io/netVizR/>
 #' @keywords internal
 "_PACKAGE"

R/layout_backbone.R

@@ -30,17 +30,13 @@ layout_as_backbone <- function(g, keep = 0.2, backbone = TRUE) {
     if (igraph::ecount(g) == 0) {
         stop("graph is empty")
     }
-
-    if (!requireNamespace("oaqc", quietly = TRUE)) {
-        stop("oaqc is needed for this function to work. Please install it.", call. = FALSE)
-    }
     if (igraph::any_multiple(g)) {
         stop("backbone layout does not work with multiple edges.")
     }
     if (igraph::is_directed(g)) {
         stop("backbone layout does not work with directed edges.")
     }
-    if (any(igraph::is.loop(g))) {
+    if (igraph::any_loop(g)) {
         stop("backbone layout does not work with loops.")
     }
 
@@ -49,11 +45,11 @@ layout_as_backbone <- function(g, keep = 0.2, backbone = TRUE) {
     }
 
     # weighting ----
-    orbs <- oaqc::oaqc(igraph::get.edgelist(g, names = FALSE) - 1, non_ind_freq = T)
+    orbs <- oaqc(igraph::as_edgelist(g, names = FALSE) - 1, non_ind_freq = T)
     e11 <- orbs$e_orbits_non_ind[, 11]
 
     qu <- rep(0, igraph::vcount(g))
-    el <- igraph::get.edgelist(g, names = FALSE)
+    el <- igraph::as_edgelist(g, names = FALSE)
     el <- cbind(el, e11)
     for (e in seq_len(nrow(el))) {
         qu[el[e, 1]] <- qu[el[e, 1]] + el[e, 3]
@@ -95,7 +91,7 @@ layout_as_backbone <- function(g, keep = 0.2, backbone = TRUE) {
 #-------------------------------------------------------------------------------
 
 umst <- function(g) {
-    el <- igraph::get.edgelist(g, names = FALSE)
+    el <- igraph::as_edgelist(g, names = FALSE)
     el <- cbind(el, igraph::E(g)$weight)
     el <- el[order(el[, 3], decreasing = TRUE), ]
     el <- cbind(el, rank(-el[, 3]))
@@ -131,7 +127,7 @@ umst <- function(g) {
 
 
 backbone_edges <- function(g, g_lay) {
-    tmp <- rbind(igraph::get.edgelist(g_lay), igraph::get.edgelist(g, names = FALSE))
+    tmp <- rbind(igraph::as_edgelist(g_lay), igraph::as_edgelist(g, names = FALSE))
     which(duplicated(tmp)) - igraph::ecount(g_lay)
 }
 
@@ -142,7 +138,7 @@ max_prexif_jaccard <- function(g) {
     el_tbl <- igraph::as_data_frame(g, "edges")
 
     N_ranks <- lapply(1:igraph::vcount(g), get_rank, el_tbl = el_tbl)
-    el <- igraph::get.edgelist(g, names = FALSE)
+    el <- igraph::as_edgelist(g, names = FALSE)
     new_w <- reweighting(el - 1, N_ranks)
     new_w
 }

R/layout_multilevel.R

@@ -75,8 +75,8 @@ layout_as_multilevel <- function(g, type = "all", FUN1, FUN2,
         if (ignore_iso) {
             iso1 <- which(igraph::degree(g1) == 0)
             iso2 <- which(igraph::degree(g2) == 0)
-            g1 <- igraph::delete.vertices(g1, iso1)
-            g2 <- igraph::delete.vertices(g2, iso2)
+            g1 <- igraph::delete_vertices(g1, iso1)
+            g2 <- igraph::delete_vertices(g2, iso2)
         }
 
         if (is.null(params1)) {
@@ -136,7 +136,7 @@ layout_as_multilevel <- function(g, type = "all", FUN1, FUN2,
 
         if (ignore_iso) {
             iso1 <- which(igraph::degree(g1) == 0)
-            g1 <- igraph::delete.vertices(g1, iso1)
+            g1 <- igraph::delete_vertices(g1, iso1)
         }
 
         if (is.null(params1)) {
@@ -182,7 +182,7 @@ layout_as_multilevel <- function(g, type = "all", FUN1, FUN2,
 
         if (ignore_iso) {
             iso2 <- which(igraph::degree(g2) == 0)
-            g2 <- igraph::delete.vertices(g2, iso2)
+            g2 <- igraph::delete_vertices(g2, iso2)
         }
 
         if (is.null(params2)) {