corrected functions cyto_create_gn_style and cyto_create_cpm_style and examples

Author: RonaldVisser

NEWS

@@ -6,6 +6,7 @@ dendroNetwork 0.5.2 (development)
 ### BUG FIXES
   * corrected bug in cyto_clean_styles()
   * corrected error in wuchwerte(). It is not using the anos1 dataset from dplR anymore
+  * corrected error in cyto_create_gn_style and cyto_create_cpm_style
 ### DEPRECATED AND DEFUNCT
   * dev-folder removed, since this was not needed (created by biocthis)
 ### DOCUMENTATION FIXES
@@ -16,6 +17,7 @@ dendroNetwork 0.5.2 (development)
   * added Vignette on Cytoscape use
   * moved information for using big datasett to seperate vignette
   * updated README: added more installion instructions
+  * corrected examples in cyto_create_gn_style and cyto_create_cpm_style
 ### CONTINUOUS INTEGRATION
 
 dendroNetwork 0.5.1 (2024-02-10)

R/cyto_create_cpm_style.R

@@ -16,6 +16,7 @@
 #' sim_table_hol <- sim_table(hol_rom)
 #' g_hol <- dendro_network(sim_table_hol)
 #' hol_com_cpm_k3 <- clique_community_names(g_hol, k = 3)
+#' cyto_create_graph(g_hol)
 #' cyto_create_cpm_style(g_hol, k = 3, com_k = hol_com_cpm_k3)
 #' }
 #'
@@ -27,7 +28,7 @@ cyto_create_cpm_style <- function(graph_input, k = 3, com_k = NULL, style_name =
     stop()
   }
   if ("GreyNodesLabel" %in% RCy3::getVisualStyleNames() == FALSE) {
-    RCy3::importVisualStyles(filename = system.file("extdata", "NetworkStyles.xml", package = "DendroNetwork"))
+    RCy3::importVisualStyles(filename = system.file("extdata", "NetworkStyles.xml", package = "dendroNetwork"))
   }
   if (is.numeric(k)) {
     if (style_name == "auto") {

R/cyto_create_gn_style.R

@@ -14,6 +14,7 @@
 #' sim_table_hol <- sim_table(hol_rom)
 #' g_hol <- dendro_network(sim_table_hol)
 #' g_hol_gn <- gn_names(g_hol)
+#' cyto_create_graph(g_hol)
 #' cyto_create_gn_style(g_hol, gn_coms = g_hol_gn)
 #' }
 #'
@@ -25,7 +26,7 @@ cyto_create_gn_style <- function(graph_input, gn_coms = NULL, style_name = "auto
     stop()
   }
   if ("GreyNodesLabel" %in% RCy3::getVisualStyleNames() == FALSE) {
-    RCy3::importVisualStyles(filename = system.file("extdata", "NetworkStyles.xml", package = "DendroNetwork"))
+    RCy3::importVisualStyles(filename = system.file("extdata", "NetworkStyles.xml", package = "dendroNetwork"))
   }
   if (style_name == "auto") {
     style_name <- paste0(substitute(graph_input), "_GN")