Update xgmml_to_gpml.R

xgmml/xgmml_to_sbml.R → xgmml/xgmml_to_gpml.R

@@ -29,11 +29,11 @@ create_Pathway <- function(name, version = date(), organism = "Homo sapiens") {
 }
 
 ### Create a GPML::DataNode object, with given label, id, type position and size
-create_DataNode <- function(label, id, type, x, y, w, h,
+create_DataNode <- function(label, id, type, x, y, w, h, color,
                             zorder = "32768", fontsize="12", valign="Middle") {
   return(read_xml(paste0("<DataNode TextLabel='", label, "' GraphId='", id, "' Type='", type, "'>",
                          "<Graphics CenterX='", x, "' CenterY='", y, "' Width='", w,
-                         "' Height='", h,"' ZOrder='", zorder,"' FontSize='", fontsize,"' Valign='", valign,"' />",
+                         "' Height='", h,"' ZOrder='", zorder,"' FontSize='", fontsize,"' Valign='", valign,"' FillColor = '", color,"'/>",
                          "<Xref Database='' ID='' />",
                          "</DataNode>")))
 }
@@ -54,7 +54,7 @@ add_DataNode_to_Pathway <- function(gpml_pathway, gpml_node) {
 }
 
 ### Add a GPML::Interaction to a GPML::Pathway, based on the ids of two GPML::DataNodes
-add_Interaction_to_Pathway <- function(gpml_pathway, id_source, id_target) {
+add_Interaction_to_Pathway <- function(gpml_pathway, id_source, id_target, color = "ffffff", thickness = "1.0") {
   dn_src <- xml_find_first(gpml_pathway, paste0("//DataNode[@GraphId='", id_source, "']"))
   dn_trg <- xml_find_first(gpml_pathway, paste0("//DataNode[@GraphId='", id_target, "']"))
   ### Identify anchor points
@@ -65,7 +65,7 @@ add_Interaction_to_Pathway <- function(gpml_pathway, id_source, id_target) {
                              "' Y='", xml_attr(xml_child(dn_trg),"CenterY"), 
                              "' GraphRef='", xml_attr(dn_trg,"GraphId"), "' RelX='-1.0' RelY='0.0' ArrowHead='Arrow'/>"))
   
-  gpml_gr <- read_xml("<Graphics ZOrder='12288' LineThickness='1.0'/>")
+  gpml_gr <- read_xml(paste0("<Graphics ZOrder='12288' LineThickness='", thickness,"' Color='", color,"'/>"))
   
   xml_add_child(gpml_gr, gpml_ps)
   xml_add_child(gpml_gr, gpml_pt)
@@ -91,15 +91,17 @@ cys_nodedata <- function(cys_node_xgmml) {
   nd_attrs <- xml_attrs(cys_node_xgmml)
   gr_attrs <- xml_attrs(xml_find_first(cys_node_xgmml, "./xgmml:graphics", ns = ns_xgmml))
   return(data.frame(id = nd_attrs["id"], label = nd_attrs["label"],
-         x = as.numeric(gr_attrs["x"]), y = as.numeric(gr_attrs["y"]), 
-         w = as.numeric(gr_attrs["w"]), h = as.numeric(gr_attrs["h"]), fill = gr_attrs["fill"]))
+                    type = xml_attrs(xml_find_first(cys_node_xgmml, "./xgmml:att[@name='mol_type']", ns = ns_xgmml))["value"],
+                    x = as.numeric(gr_attrs["x"]), y = as.numeric(gr_attrs["y"]),
+                    w = as.numeric(gr_attrs["w"]), h = as.numeric(gr_attrs["h"]), fill = gr_attrs["fill"]))
 }
 
 ### Read edge information from the CytoScape XGMML file
 cys_edgedata <- function(cys_edge_xgmml) {
   eg_attrs <- xml_attrs(cys_edge_xgmml)
+  gr_attrs <- xml_attrs(xml_find_first(cys_edge_xgmml, "./xgmml:graphics", ns = ns_xgmml))
   return(data.frame(id = eg_attrs["id"], label = eg_attrs["label"],
-                    source = eg_attrs["source"], target = eg_attrs["target"]))
+                    source = eg_attrs["source"], target = eg_attrs["target"], color = gr_attrs["fill"], thickness = gr_attrs["width"]))
 }
 
 ### The main function to call, optionally generating an image of the created diagram 
@@ -117,9 +119,6 @@ xgmml_gpml <- function(xgmml_file, output,
   ### Correct for x,y negative values, add 100 margin
   nodedata$x <- nodedata$x + abs(min(nodedata$x)) + 100
   nodedata$y <- nodedata$y + abs(min(nodedata$y)) + 100
-  nodedata <- cbind(nodedata, type = "Pathway")
-  nodedata$type[grep("^[A-Z0-9]{3,}$",nodedata$label)] <- "Protein"
-  nodedata$type[grep("_[1-9]",nodedata$label)] <- "Metabolite"
   
   edgedata <- do.call("rbind", lapply(xml_find_all(xgmml, "//xgmml:edge", ns = ns_xgmml), cys_edgedata))
   ### Purely numeric ids are a problem, adding a letter
@@ -132,10 +131,12 @@ xgmml_gpml <- function(xgmml_file, output,
   apply(nodedata, 1, function(x)
     add_DataNode_to_Pathway(xgmml_P, 
                             create_DataNode(label = x["label"], id = x["id"], type = x["type"],
-                                            x = x["x"], y = x["y"], w = x["w"], h = x["h"])))
+                                            x = x["x"], y = x["y"], w = x["w"], h = x["h"], 
+                                            color = tolower(substr(x["fill"], 2, 7)))))
   
   apply(edgedata, 1, function(x) 
-    add_Interaction_to_Pathway(xgmml_P, x["source"], x["target"]))
+    add_Interaction_to_Pathway(xgmml_P, x["source"], x["target"], 
+                               color = tolower(substr(x["color"], 2, 7)), thickness = x["thickness"]))
   
   write_Pathway(xgmml_P, filename = output)
   
@@ -154,4 +155,4 @@ xgmml_gpml <- function(xgmml_file, output,
   }
   
   invisible(0)
-}
\ No newline at end of file
+}