@@ -1,16 +1,31 @@

 Package: ROntoTools

 Type: Package

 Title: R Onto-Tools suite

-Version: 1.7.0

-Author: Calin Voichita <calin@wayne.edu> and Sorin Draghici

-        <sorin@wayne.edu>

+Version: 1.7.1

+Author: Calin Voichita <calin@wayne.edu> and Sorin Draghici <sorin@wayne.edu>

 Maintainer: Calin Voichita <calin@wayne.edu>

 Description: Suite of tools for functional analysis

+biocViews: NetworkAnalysis, Microarray, GraphsAndNetworks

 License: GPL (>= 3)

-Depends: methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz

-Suggests: RUnit, BiocGenerics

-Collate: 'pathwayExpress.R' 'utils.R' 'graphWeights.R' 'keggDataREST.R'

-        'AllClasses.R' 'AllGenerics.R' 'nodeWeights-methods.R'

-        'pePathway-utils.R' 'Summary-methods.R' 'plot-methods.R'

-        'renderInfo-methods.R'

-biocViews: Network, Microarray, GraphAndNetwork

+Depends:

+    methods,

+    graph,

+    boot,

+    KEGGREST,

+    KEGGgraph,

+    Rgraphviz

+Suggests:

+    RUnit,

+    BiocGenerics

+Collate:

+    'pathwayExpress.R'

+    'utils.R'

+    'graphWeights.R'

+    'keggDataREST.R'

+    'AllClasses.R'

+    'AllGenerics.R'

+    'nodeWeights-methods.R'

+    'pePathway-utils.R'

+    'Summary-methods.R'

+    'plot-methods.R'

+    'renderInfo-methods.R'

@@ -23,17 +23,11 @@ loadKEGGpathwayDataREST <- function(organism = "hsa",

     allPathwayInfo <- lapply(names(pathList), 

                              function(pathID) {

-                               

                                p <- keggGet(pathID, "kgml")

-                               

                                pKgml <- file.path(tmpDir, paste(strsplit(pathID, ":")[[1]][2], ".kgml", sep = ""))

-                               

                                write(p, pKgml)

-                               

                                pathData <- parseKGML(pKgml)

-                               

                                file.remove(pKgml)

-                               

                                if(verbose)

                                  setTxtProgressBar(pb, getTxtProgressBar(pb) + 1)

                                return(pathData)

@@ -98,7 +92,7 @@ keggPathwayGraphs <- function(organism = "hsa",

                               verbose = TRUE)

 {

   defaultParameters <- FALSE

-  if ((organism == "hsa") & all(targRelTypes == c("GErel","PCrel","PPrel")) &

+  if ((organism == "hsa") & all(targRelTypes %in% c("GErel","PCrel","PPrel")) &

         (relPercThresh == 0.9) & (nodeOnlyGraphs == FALSE))

     defaultParameters <- TRUE  

@@ -124,8 +118,10 @@ keggPathwayGraphs <- function(organism = "hsa",

   counts <- do.call(rbind,lapply(l, function(x) as.vector(x[allRelTypes])))

   colnames(counts) <- allRelTypes

+  counts[is.na(counts)] <- 0

+  

   accIndex <- rowSums(counts[,targRelTypes], na.rm=T) / rowSums(counts, na.rm=T) >= relPercThresh

-  accIndex[is.na(accIndex)] <- FALSE  

+  accIndex[is.na(accIndex)] <- nodeOnlyGraphs

   allPathwayInfo <- allPathwayInfo[accIndex]

   names(allPathwayInfo) <- sapply(allPathwayInfo, getName)

@@ -138,24 +134,45 @@ keggPathwayGraphs <- function(organism = "hsa",

   pathwayGraphs <- lapply(allPathwayInfo, function(g) 

   {

-    g <- KEGGgraph::KEGGpathway2Graph(g)

-    kg <- new("graphNEL", nodes(g), edges(g), edgemode = "directed")

+#     tryCatch(

+      g <- KEGGpathway2Graph(g, expandGenes=TRUE)

+#       , error = function(e) {})    

+    if (class(g) != "graphNEL") {

+      return(NULL)

+    }

+    

+    kg <- new("graphNEL", nodes(g), edges(g), edgemode = "directed")

+

     if (length(getKEGGedgeData(g)) == 0)

     {

       if (verbose)

         setTxtProgressBar(pb, getTxtProgressBar(pb) + 1)

-      return(NULL)

+      if (nodeOnlyGraphs)

+        return(kg)

+      else

+        return(NULL)

     }

-    edgeDataDefaults(kg, "subtype") <- NA  

-        

-    relGeneTable <- data.frame(cbind(

+    edgeDataDefaults(kg, "subtype") <- NA

+    

+

+    cf <- cbind(

       do.call(rbind, strsplit(names(getKEGGedgeData(g)), '~')),

       sapply(getKEGGedgeData(g), function(e) 

         paste(lapply(getSubtype(e), getName), collapse=","))

-    ), stringsAsFactors = FALSE)

+    );

+

+    if (nrow(cf) < 2) {

+      ucf <- cf

+    } else {

+      ucf <- cf[unique(rownames(cf)),]

+      ucf[,3] <- tapply(cf[,3], rownames(cf), function(ll) return(paste( unique(ll), collapse = ',')))[rownames(ucf)]

+    }

+    

+

+    relGeneTable <- data.frame(ucf, stringsAsFactors = FALSE)

     names(relGeneTable) <- c("from","to","subtype")

-        

+

     edgeData(kg, relGeneTable$from, relGeneTable$to, "subtype") <- relGeneTable$subtype

     if (verbose)

@@ -213,3 +230,86 @@ keggPathwayNames <- function(organism = "hsa",

   return(allNames)

 }

+#' Modified version of the same function from KEGGgraph

+#' 

+#' @keywords internal

+KEGGpathway2Graph <- function (pathway, genesOnly = TRUE, expandGenes = TRUE) 

+{

+  stopifnot(is(pathway, "KEGGPathway"))

+  pathway <- splitKEGGgroup(pathway)

+  if (expandGenes) {

+    pathway <- expandKEGGPathway(pathway)

+  }

+  knodes <- nodes(pathway)

+  kedges <- unique(edges(pathway))

+  node.entryIDs <- getEntryID(knodes)

+  edge.entryIDs <- getEntryID(kedges)

+  V <- node.entryIDs

+  edL <- vector("list", length = length(V))

+  names(edL) <- V

+  if (is.null(nrow(edge.entryIDs))) {

+    for (i in seq(along = edL)) {

+      edL[[i]] <- list()

+    }

+  }

+  else {

+    for (i in 1:length(V)) {

+      id <- node.entryIDs[i]

+      hasRelation <- id == edge.entryIDs[, "Entry1ID"]

+      if (!any(hasRelation)) {

+        edL[[i]] <- list(edges = NULL)

+      }

+      else {

+        entry2 <- unname(edge.entryIDs[hasRelation, "Entry2ID"])

+        edL[[i]] <- list(edges = entry2)

+      }

+    }

+  }

+  gR <- new("graphNEL", nodes = V, edgeL = edL, edgemode = "directed")

+  names(kedges) <- sapply(kedges, function(x) paste(getEntryID(x), 

+                                                    collapse = "~"))

+  env.node <- new.env()

+  env.edge <- new.env()

+  assign("nodes", knodes, envir = env.node)

+  assign("edges", kedges, envir = env.edge)

+  nodeDataDefaults(gR, "KEGGNode") <- env.node

+  edgeDataDefaults(gR, "KEGGEdge") <- env.edge

+  if (genesOnly) {    

+    gR <- subGraphByNodeType(gR, "gene")

+  }

+  return(gR)

+}

+

+#' Modified version of the same function from KEGGgraph

+#' 

+#' @keywords internal

+subGraphByNodeType <- function (graph, type = "gene") 

+{

+  kegg.node.data <- getKEGGnodeData(graph)

+  types <- sapply(kegg.node.data, getType)

+  isType <- grep(type, types)

+  if (!any(isType)) {

+    stop("No '", type, "' type found in the file, maybe it is a map file. Please try parsing the file with 'genesOnly=FALSE'\n")

+  }

+  new.nodes <- names(types[isType])

+  new.edges <- edges(graph)

+  new.edges <- new.edges[names(new.edges) %in% new.nodes]

+  new.edges <- lapply(new.edges, function(eL) return(eL[eL %in% new.nodes]))

+  

+  subgraph <- new("graphNEL", new.nodes, new.edges, edgemode = "directed")

+    

+  subnodes <- new.nodes

+  subedges <- getRgraphvizEdgeNames(subgraph)

+  keggnodes <- get("nodes", nodeDataDefaults(graph, "KEGGNode"))

+  keggedges <- get("edges", edgeDataDefaults(graph, "KEGGEdge"))

+  subkeggnodes <- keggnodes[subnodes]

+  subkeggedges <- keggedges[subedges]

+  env.node <- new.env()

+  env.edge <- new.env()

+  assign("nodes", subkeggnodes, envir = env.node)

+  assign("edges", subkeggedges, envir = env.edge)

+  nodeDataDefaults(subgraph, "KEGGNode") <- env.node

+  edgeDataDefaults(subgraph, "KEGGEdge") <- env.edge

+  

+  return(subgraph)

+}

@@ -197,7 +197,7 @@ pe.boot <- function(g, x, ref, nboot, all.genes = F)

   if (length(pePath@input) == 0)

     return(NULL)

-  if (is.null(inv))

+  if (is.null(inv) || (numEdges(g) == 0))

   {

     pePath@asGS <- TRUE

     return(pePath)

@@ -270,4 +270,4 @@ compute.B <- function(g, non.zero = TRUE)

   return(B)

 }

-  

+  

\ No newline at end of file

Binary files a/inst/extdata/KEGGRESTunparsed_hsa.RData and b/inst/extdata/KEGGRESTunparsed_hsa.RData differ

Binary files a/inst/extdata/kpgDefault.RData and b/inst/extdata/kpgDefault.RData differ

@@ -1,4 +1,5 @@

 \name{Summary}

+\alias{Summary}

 \alias{Summary,peRes-method}

 \alias{Summary.peRes}

 \title{Summarize the results of a Pathway-Express analysis}