added object checks to functions

Author: RonaldVisser

NEWS.md

@@ -7,6 +7,8 @@
 ### Minor improvements
 
 -   added a CONTRIBUTING.md file for contribution guidelines
+-   added check to determine if input graph is an igraph object for all functions that need an igraph as input
+-   added check to determine if input tree-ring dataset is rwl object for `sim_table`
 
 ### Bug Fixes
 

R/clique_community_names.R

@@ -25,6 +25,9 @@
 #' @importFrom magrittr %>%
 
 clique_community_names <- function(g, k = 3) {
+  if (!igraph::is.igraph(g)) {
+    stop(paste0("Please use an igraph object as input. The current object is an ", class(g), "."))
+  }
   if (k > igraph::clique_num(g)) {
     stop(paste0("The maximum clique size in the network is ", igraph::clique_num(g), ". Therefore k cannot exceed this number"))
   }

R/clique_community_names_par.R

@@ -30,6 +30,9 @@
 #' @importFrom foreach %dopar%
 
 clique_community_names_par <- function(g, k = 3, n_core = 4) {
+  if (!igraph::is.igraph(g)) {
+    stop(paste0("Please use an igraph object as input. The current object is an ", class(g), "."))
+  }
   doParallel::registerDoParallel(cores = n_core)
   if (k > igraph::clique_num(g)) {
     stop(paste0("The maximum clique size in the network is ", igraph::clique_num(g), ". Therefore k cannot exceed this number"))

R/cyto_create_cpm_style.R

@@ -30,6 +30,9 @@ cyto_create_cpm_style <- function(graph_input, k = 3, com_k = NULL, style_name =
   if ("GreyNodesLabel" %in% RCy3::getVisualStyleNames() == FALSE) {
     RCy3::importVisualStyles(filename = system.file("extdata", "NetworkStyles.xml", package = "dendroNetwork"))
   }
+  if (!igraph::is.igraph(graph_input)) {
+    stop(paste0("Please use an igraph object as input. The current object is an ", class(graph_input), "."))
+  }
   if (is.numeric(k)) {
     if (style_name == "auto") {
       style_name <- paste0(substitute(graph_input), "_CPM(k=", k, ")")

R/cyto_create_gn_style.R

@@ -28,6 +28,9 @@ cyto_create_gn_style <- function(graph_input, gn_coms = NULL, style_name = "auto
   if ("GreyNodesLabel" %in% RCy3::getVisualStyleNames() == FALSE) {
     RCy3::importVisualStyles(filename = system.file("extdata", "NetworkStyles.xml", package = "dendroNetwork"))
   }
+  if (!igraph::is.igraph(graph_input)) {
+    stop(paste0("Please use an igraph object as input. The current object is an ", class(graph_input), "."))
+  }
   if (style_name == "auto") {
     style_name <- paste0(substitute(graph_input), "_GN")
   }

R/cyto_create_graph.R

@@ -33,6 +33,9 @@ cyto_create_graph <- function(graph_input,
     message("Cytoscape is not running, please start Cytoscape first")
     stop()
   }
+  if (!igraph::is.igraph(graph_input)) {
+    stop(paste0("Please use an igraph object as input. The current object is an ", class(graph_input), "."))
+  }
   varnames <- all.vars(match.call())
   for (v in varnames) {
     if (!exists(v)) {

R/find_all_cpm_com.R

@@ -17,6 +17,9 @@
 
 
 find_all_cpm_com <- function(graph_input, n_core = 0) {
+  if (!igraph::is.igraph(graph_input)) {
+    stop(paste0("Please use an igraph object as input. The current object is an ", class(graph_input), "."))
+  }
   if (n_core > 1) {
     for (i in 3:igraph::clique_num(graph_input)) {
       com_cpm <- clique_community_names_par(graph_input, i, n_core)

R/gn_names.R

@@ -18,6 +18,9 @@
 #' @importFrom magrittr %>%
 
 gn_names <- function(g) {
+  if (!igraph::is.igraph(g)) {
+    stop(paste0("Please use an igraph object as input. The current object is an ", class(g), "."))
+  }
   g_GN <- igraph::cluster_edge_betweenness(g,
     weights = igraph::E(g)$weight, directed = FALSE,
     edge.betweenness = TRUE, merges = TRUE, bridges = TRUE,

R/sim_table.R

@@ -33,6 +33,14 @@ sim_table <- function(trs1,
                       trs2 = NULL,
                       min_overlap = 50,
                       last_digit_radius = FALSE) {
+  if (!("rwl" %in% class(trs1))) {
+    stop(paste0("Please use an rwl object as input. The current first input object is a ", class(trs1), "."))
+  }
+  if (!is.null(trs2)) {
+    if (!"rwl" %in% class(trs2)) {
+      stop(paste0("Please use an rwl object as input. The current second input object is a ", class(trs2), "."))
+    }
+  }
   # nr of series in tree-ring series
   n1 <- dim(trs1)[2]
   if (is.null(trs2)) {