@@ -1,14 +1,31 @@

 Package: ROntoTools

 Type: Package

 Title: R Onto-Tools suite

-Version: 0.99.2

+Version: 0.99.3

 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: R (>= 3.0.0), methods, graph, boot, KEGGREST, KEGGgraph

-Suggests: RUnit, BiocGenerics, Rgraphviz

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

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

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

+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'

@@ -1,13 +1,18 @@

 export(alpha1MR)

 export(alphaMLG)

+export(compute.fischer)

+export(compute.normalInv)

 export(keggPathwayGraphs)

 export(keggPathwayNames)

 export(pe)

+export(peEdgeRenderInfo)

+export(peNodeRenderInfo)

 export(setEdgeWeights)

 export(setNodeWeights)

 exportClasses(pePathway)

 exportClasses(peRes)

 exportMethods(nodeWeights)

+exportMethods(plot)

 exportMethods(Summary)

 import(boot)

 import(graph)

@@ -21,7 +21,7 @@

 #' 

 #' Calin Voichita and Sorin Draghici

 #'

-#' @seealso \code{\link{pe}} \code{\link{pePathway}}

+#' @seealso \code{\link{pe}}, \code{\link{pePathway}}

 #'

 #' @aliases peRes-class

 #' @exportClass peRes

@@ -39,12 +39,12 @@ setClass("peRes",

 #' @section Slots:

 #' 

 #' \describe{

-#'    \item{map}{an object of type graph (e.g., \code{\link{graphNEL}}).}

-#'    \item{input}{named vector of fold changes for genes on this pathway. The names of the genes are the orignal IDS used in the analysis}

-#'    \item{ref}{vector of reference IDs on this pathway}

-#'    \item{boot}{an object of class \code{boot} encoding the bootstrap information.}

-#'    \item{PF}{the gene perturbation factors for all genes on the pathway, as computed by Pathway-Express.}

-#'    \item{Acc}{the gene accumulations for all genes on the pathway, as computed by Pathway-Express.}

+#'    \item{\code{map}:}{an object of type graph (e.g., \code{\link{graphNEL}}).}

+#'    \item{\code{input}:}{named vector of fold changes for genes on this pathway. The names of the genes are the orignal IDS used in the analysis}

+#'    \item{\code{ref}:}{vector of reference IDs on this pathway}

+#'    \item{\code{boot}:}{an object of class \code{boot} encoding the bootstrap information.}

+#'    \item{\code{Pert}:}{the gene perturbation factors for all genes on the pathway, as computed by Pathway-Express.}

+#'    \item{\code{Acc}:}{the gene accumulations for all genes on the pathway, as computed by Pathway-Express.}

 #' }

 #' 

 #' @author

@@ -52,7 +52,7 @@ setClass("peRes",

 #' Calin Voichita and Sorin Draghici

 #'

 #'             

-#' @seealso \code{\link{pe}} \code{\link{peRes}}

+#' @seealso \code{\link{pe}}, \code{\link{peRes}}

 #' 

 #' @aliases pePathway-class

 #' @import graph

@@ -62,7 +62,7 @@ setClass("pePathway",

                         input = "numeric",

                         ref = "character",

                         boot = "ANY",

-                        PF = "numeric",

+                        Pert = "numeric",

                         Acc = "numeric"

          ), 

          prototype(map = new("graphNEL")

@@ -32,7 +32,7 @@

 #' 

 #' @seealso

 #' 

-#' \link{nodes} \link{nodeData}

+#' \link{nodes}, \link{nodeData}

 #' 

 #' @examples

 #' 

@@ -43,7 +43,6 @@

 #' nodeWeights(g, "B")

 #' nodeWeights(g, attr = "WT", default = 3)

 #' 

-#' @docType methods

 #' @rdname nodeWeights

 #' 

 #' @export

@@ -47,7 +47,9 @@

 #' head(Summary(peRes, pathNames = kpn, totalAcc = FALSE, totalPert = FALSE, 

 #'              pAcc = FALSE, pORA = FALSE, comb.pv = NULL, order.by = "pPert"))

 #' 

+#' @rdname Summary-methods

 #' 

+#' @aliases Summary.peRes

 #' @aliases Summary,peRes-method

 #' @export

 setMethod("Summary", c("x" = "peRes"),

@@ -74,9 +76,7 @@ setMethod("Summary", c("x" = "peRes"),

               pStats$pPert <- ifelse(pPert, compute.pPert(pePath), NULL)

               pStats$pAcc <- ifelse(pAcc, compute.pAcc(pePath), NULL)

-              if (pORA & peRes@cutOffFree)

-                warning("The over-representaion p-value is not defined for cut-off free analysis and will not be computed!")  

-              pStats$pORA <- ifelse(pORA & !peRes@cutOffFree, compute.pORA(pePath, length(peRes@input), length(peRes@ref)), NULL)

+              pStats$pORA <- ifelse(pORA & !x@cutOffFree, compute.pORA(pePath, length(x@input), length(x@ref)), NULL)

               pStats$pComb <- ifelse(!is.null(comb.pv) & !any(is.null(pStats[comb.pv])), 

                                      as.numeric(comb.pv.func(unlist(pStats[comb.pv]))), NULL)

@@ -84,6 +84,17 @@ setMethod("Summary", c("x" = "peRes"),

               return(unlist(pStats))

             }

+            if (pORA & x@cutOffFree)

+            {

+              pORA <- FALSE

+              if ("pORA" %in% comb.pv)

+              {

+                order.by <- setdiff(comb.pv, "pORA")[1]

+                comb.pv <- NULL

+              }

+              message("The over-representaion p-value is not defined for cut-off free analysis and will not be computed!")  

+            }

+            

             if(!is.null(comb.pv))

             {

               if(!all(comb.pv %in% c("pPert","pAcc","pORA")))

@@ -98,7 +109,7 @@ setMethod("Summary", c("x" = "peRes"),

               }

             }

-            topStats <- data.frame(do.call(rbind, lapply(peRes@pathways, pathStats)))

+            topStats <- data.frame(do.call(rbind, lapply(x@pathways, pathStats)))

             if(!is.null(pathNames))

             {

@@ -58,7 +58,7 @@ loadKEGGpathwayDataREST <- function(organism = "hsa",

 #' @param targRelTypes target relation types

 #' @param relPercThresh percentage of the number of relation types over all possible realtions in the pathway

 #' @param nodeOnlyGraphs allow graphs with no edges

-#' @param updateCache re-downlaod KEGG data

+#' @param updateCache re-download KEGG data

 #' @param verbose show progress of downloading and parsing

 #' 

 #' @return

@@ -194,7 +194,7 @@ keggPathwayGraphs <- function(organism = "hsa",

 #' 

 #' # to update the pathway cache for human run:

 #' # kpn <- keggPathwayNames("hsa", updateCache = TRUE)

-#' # this is time consuming and depends on the available bandwith.

+#' # this is time consuming and depends on the available bandwidth.

 #' 

 #' head(kpn)

 #' 

@@ -2,7 +2,7 @@

 #' 

 #' 

 #' @param x named vector of log fold changes for the differentially expressed genes; \code{names(x)} must use the same id's as \code{ref} and the nodes of the \code{graphs}

-#' @param graphs list of pathway graphs as objects of type \code{graph} (e.g., \code{\link{graphNEL}}); the graphs must be weighted graphs (i.e., have an atrribute \code{weight} for both nodes and edges)

+#' @param graphs list of pathway graphs as objects of type \code{graph} (e.g., \code{\link{graphNEL}}); the graphs must be weighted graphs (i.e., have an attribute \code{weight} for both nodes and edges)

 #' @param ref the reference vector for all genes in the analysis; if the reference is not provided or it is identical to \code{names(x)} a cut-off free analysis is performed

 #' @param nboot number of bootstrap iterations

 #' @param verbose print progress output

@@ -31,7 +31,8 @@

 #' 

 #' Draghici S., Khatri P., Tarca A.L., Amin K., Done A., Voichita C., Georgescu C., Romero R.: "A systems biology approach for pathway level analysis". Genome Research, 17, 2007. 

 #' 

-#' @seealso \code{\link{Summary}} \code{\link{keggPathwayGraphs}} \code{\link{setNodeWeights}} \code{\link{setEdgeWeights}}

+#' @seealso \code{\link{Summary}}, \code{\link{plot.peRes}}, 

+#' \code{\link{keggPathwayGraphs}}, \code{\link{setNodeWeights}}, \code{\link{setEdgeWeights}}

 #' 

 #' @examples

 #' 

@@ -223,8 +224,8 @@ pe.boot <- function(g, x, ref, nboot, all.genes = F)

   xx <- rep(0, nrow(inv))

   names(xx) <- rownames(inv)

   xx[names(pePath@input)] <- pePath@input  

-  pePath@PF = (inv %*% xx)[,1];

-  pePath@Acc = pePath@PF - xx

+  pePath@Pert = (inv %*% xx)[,1];

+  pePath@Acc = pePath@Pert - xx

   return(pePath) 

 }

new file mode 100644

@@ -0,0 +1,221 @@

+#' Plot pathway level statistics

+#' 

+#' @description Display graphical representation of pathway level statistic like:

+#' i) two way comparison between the measured expression change and one of the 

+#' factors computed by Pathway-Express (\code{\link{pe}}) or ii) the boostrap 

+#' statistics of the same factors.

+#' 

+#' 

+#' @param x an object of type \code{\link{pePathway}}

+#' @param y if provided, the factor to be ploted (either \code{Acc} (default) or \code{Pert}; see \code{\link{pePathway}})

+#' @param ... Arguments to be passed to methods, such as \code{\link{par}}

+#' @param type type of plot (either \code{two.way} (default) or \code{boot})

+#' @param eps any value smaller than this will be ploted as 0

+#' 

+#' @author Calin Voichita and Sorin Draghici

+#' 

+#' @seealso \code{\link{pe}}, \code{\link{plot.peRes}}, \code{\link{peNodeRenderInfo}}, \code{\link{peEdgeRenderInfo}}

+#' 

+#' @examples

+#' 

+#' # load experiment

+#' load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))

+#' fc <- top$logFC[top$adj.P.Val <= .01]

+#' names(fc) <- top$entrez[top$adj.P.Val <= .01]

+#' ref <- top$entrez

+#' 

+#' # load the set of pathways

+#' kpg <- keggPathwayGraphs("hsa")

+#' kpg <- setEdgeWeights(kpg)

+#' kpg <- setNodeWeights(kpg, defaultWeight = 1)

+#' 

+#' # perform the pathway analysis (for more accurate results use nboot = 2000)

+#' peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)

+#' 

+#' plot(peRes@@pathways[[50]])

+#' 

+#' plot(peRes@@pathways[[50]], "Pert", main = "Perturbation factor")

+#' 

+#' plot(peRes@@pathways[[50]], type = "boot")

+#' 

+#' plot(peRes@@pathways[[50]], "Pert", type = "boot", main = "Perturbation factor")

+#' 

+#' @rdname plot.pePathway-methods

+#' @name plot.pePathway

+#' 

+#' @aliases plot.pePathway

+#' @aliases plot,pePathway,missing-method

+#' @export

+setMethod("plot", signature(x="pePathway", y="missing"),

+          function(x, y, ..., type = "two.way", eps = 1e-6)

+          {

+            plot(x, y = "Acc", ..., type = type, eps = eps)           

+          }

+)

+

+#' @rdname plot.pePathway-methods

+#' 

+#' @aliases plot.pePathway

+#' @aliases plot,pePathway,character-method

+#' @export

+setMethod("plot", signature(x="pePathway", y="character"),

+          function(x, y, main = "", ... , type = "two.way", eps = 1e-6)

+          {

+            if (!(y %in% c("Acc", "Pert")))

+              stop("Undefined slot selected: ", y,".")

+                        

+            switch(type,

+                   two.way={        

+                     iy <- y

+                     

+                     extInput <- rep(0, length(slot(x, iy)))

+                     names(extInput) <- names(slot(x, iy))

+                     extInput[names(x@input)] <- x@input

+                     

+                     cl <- rep("black", length(slot(x, iy)))

+                     cl[abs(slot(x, iy)) >= eps] <- "green"

+                     cl[abs(extInput) >= eps] <- "blue"

+                     cl[abs(slot(x, iy)) >= eps & abs(extInput) >= eps] <- "red"

+                     

+                     plot(slot(x, iy), extInput, pch = 16, xlab = y, ylab = "Log2 FC", main = main, ...)

+                     abline(v=0,h=0, lwd = .5)

+                     points(slot(x, iy), extInput, pch = 16, col = cl)

+                     

+                     return(invisible())

+                   },

+                   boot={

+                     iy <- paste("t", y, sep = "")

+                     

+                     tB <- x@boot$t0[iy]

+                     allB <- x@boot$t[,iy]

+                     

+                     tB <- (tB - mean(allB)) / sd(allB)

+                     allB <- (allB - mean(allB)) / sd(allB)

+                     

+                     plot(density(allB), xlab = y, main = main, ...)

+                     abline(v=0, lwd = .5)

+                     abline(v=tB, lwd = 1, col = "red")

+                     

+                     return(invisible())

+                   }

+            )

+            stop(type, " is not a valid plot type.")

+            

+          }

+)

+

+#' Plot Pathway-Express result

+#' 

+#' @description Display a two-way plot using two of the p-values from the Pathway-Express analysis.

+#' 

+#' @param x an object of type \code{\link{peRes}}

+#' @param y vector of two p-values names to be combined using \code{comb.pv.func} (default: \code{c("pAcc", "pORA")}).

+#' @param ... Arguments to be passed to methods, such as \code{\link{par}}.

+#' @param comb.pv.func the function to combine the p-values - takes as input a vector of p-values 

+#' and returns the combined p-value (default: \code{\link{compute.fischer}}).

+#' @param adjust.method the name of the method to adjust the p-value (see \code{\link{p.adjust}})

+#' @param threshold corrected p-value threshold

+#' @param eps any value smaller than this will be considered as \code{eps} (default: \code{1e-6}).

+#' 

+#' @author Calin Voichita and Sorin Draghici

+#' 

+#' @seealso \code{\link{pe}}, \code{\link{Summary.peRes}}, \code{\link{plot.pePathway}}

+#' 

+#' @examples

+#' 

+#' # load experiment

+#' load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))

+#' fc <- top$logFC[top$adj.P.Val <= .01]

+#' names(fc) <- top$entrez[top$adj.P.Val <= .01]

+#' ref <- top$entrez

+#' 

+#' # load the set of pathways

+#' kpg <- keggPathwayGraphs("hsa")

+#' kpg <- setEdgeWeights(kpg)

+#' kpg <- setNodeWeights(kpg, defaultWeight = 1)

+#' 

+#' # perform the pathway analysis (for more accurate results use nboot = 2000)

+#' peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)

+#' 

+#' plot(peRes)

+#' 

+#' plot(peRes, c("pPert","pORA"), comb.pv.func = compute.normalInv, threshold = .01)

+#' 

+#' @rdname plot.peRes-methods

+#' @name plot.peRes

+#' 

+#' @aliases plot.peRes

+#' @aliases plot,peRes,missing-method

+#' @export

+setMethod("plot", signature(x="peRes", y="missing"),

+          function(x, y, ... , comb.pv.func = compute.fischer, adjust.method = "fdr", threshold = .05, eps = 1e-6)

+          {

+            plot(x, y = c("pAcc", "pORA"), ... , comb.pv.func = comb.pv.func, adjust.method = adjust.method,

+                 threshold = threshold, eps = eps)

+          }

+)

+

+#' @rdname plot.peRes-methods

+#' 

+#' @aliases plot.peRes

+#' @aliases plot,peRes,character-method

+#' @export

+setMethod("plot", signature(x="peRes", y="character"),

+          function(x, y, ... , comb.pv.func = compute.fischer, adjust.method = "fdr", threshold = .05, eps = 1e-6)

+          {

+            

+            st <- Summary(x, comb.pv = y, comb.pv.func = comb.pv.func, adjust.method = adjust.method)

+            st <- st[!is.na(st[, paste("pComb", adjust.method, sep = ".")]),]

+            

+            st[,y[1]][st[,y[1]] <= eps] <- eps

+            st[,y[2]][st[,y[2]] <= eps] <- eps

+            

+            i <- st[, paste("pComb", adjust.method, sep = ".")] <= threshold

+            thr.comb <- mean(min(st[!i,"pComb"]),max(st[i,"pComb"]))

+            

+            xrange <- c(min(-log(st[,y[1]])), max(-log(st[,y[1]])))

+            xrange[2] <- xrange[2] + (xrange[2]-xrange[1]) * .1

+            yrange <- c(min(-log(st[,y[2]])), max(-log(st[,y[2]]))) 

+            yrange[2] <- yrange[2] + (yrange[2]-yrange[1]) * .1

+            

+            i <- seq(xrange[1], xrange[2], length.out=200)

+            j <- seq(yrange[1], yrange[2], length.out=200)

+            expGrid <- expand.grid(i,j)

+            z <- apply(1/exp(expGrid), 1, comb.pv.func) <= thr.comb

+            

+            plot(c(min(-log(st[,y[1]])),min(-log(st[,y[2]]))), 

+                 xlab = y[1], ylab = y[2], 

+                 xlim = xrange,

+                 ylim = yrange,

+                 col = "white", ...)

+            nonSig <- expGrid[!z,][chull(expGrid[!z,]),]

+            sig <- expGrid[z,][chull(expGrid[z,]),]

+            

+            polygon(nonSig, col="gray90")

+            polygon(sig, col="lightcyan")

+            

+            i <- st[, paste("pComb", adjust.method, sep = ".")] <= threshold

+            

+            points(-log(st[,y[1]]), -log(st[,y[2]]),  xlab = y[1], ylab = y[2], pch = 19)

+            if (any(i))

+            {

+              points(-log(st[,y[1]])[i], -log(st[,y[2]])[i], pch = 21, bg = "red")

+              text(-log(st[,y[1]])[i], -log(st[,y[2]])[i] - .5, labels = rownames(st)[i], 

+                   cex = .75)

+            }

+            

+            i <- st[, paste(y[1], adjust.method, sep = ".")] <= threshold

+            if (any(i))

+            {              

+              thr1 <- mean(min(st[!i,y[1]]),max(st[i,y[1]]))            

+              abline(v = -log(thr1), col = "red", lwd = 2, lty = 2)

+            }

+            

+            i <- st[, paste(y[2], adjust.method, sep = ".")] <= threshold

+            if (any(i))

+            {

+              thr2 <- mean(min(st[!i,y[2]]),max(st[i,y[2]]))                        

+              abline(h = -log(thr2), col = "red", lwd = 2, lty = 2)

+            }

+          }

+)

new file mode 100644

@@ -0,0 +1,151 @@

+#' Extract edge render information from a \code{pePathway} object

+#' 

+#' @param x an object of class \code{\link{pePathway}}

+#' @param pos.col color of the edges with possitive weight

+#' @param pos.lty line type of the edges with possitive weight

+#' @param pos.ah arrow head of the edges with possitive weight 

+#' @param neg.col color of the edges with negative weight

+#' @param neg.lty line type of the edges with negative weight 

+#' @param neg.ah arrow head of the edges with negative weight 

+#' @param zero.col color of the edges with zero weight 

+#' @param zero.lty color of the edges with zero weight

+#' @param zero.ah color of the edges with zero weight

+#' 

+#' @value a named list as expected by \code{\link{edgeRenderInfo}}

+#' 

+#' @author Calin Voichita and Sorin Draghici

+#' 

+#' @seealso \code{\link{edgeRenderInfo}},\code{\link{par}}

+#' 

+#' @examples

+#' 

+#' # load experiment

+#' load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))

+#' fc <- top$logFC[top$adj.P.Val <= .01]

+#' names(fc) <- top$entrez[top$adj.P.Val <= .01]

+#' ref <- top$entrez

+#' 

+#' # load the set of pathways

+#' kpg <- keggPathwayGraphs("hsa")

+#' kpg <- setEdgeWeights(kpg)

+#' kpg <- setNodeWeights(kpg, defaultWeight = 1)

+#' 

+#' # perform the pathway analysis

+#' peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)

+#' 

+#' p <- peRes@@pathways[[50]]

+#' g <- layoutGraph(p@@map, layoutType = "dot")

+#' graphRenderInfo(g) <- list(fixedsize = FALSE)

+#' edgeRenderInfo(g) <- peEdgeRenderInfo(p)

+#' nodeRenderInfo(g) <- peNodeRenderInfo(p)

+#' # notice the different type of edges in the graph (solid/dashed/dotted) 

+#' renderGraph(g)

+#' 

+#' @export

+peEdgeRenderInfo <- function(x,

+                             pos.col = "black", pos.lty = "solid", pos.ah = "vee",

+                             neg.col = "black", neg.lty = "dashed", neg.ah = "tee",

+                             zero.col = "lightgray", zero.lty = "dotted", zero.ah = "none")

+{

+  stopifnot(class(x) == "pePathway")

+  

+  ew <- unlist(edgeWeights(x@map))

+  

+  aHead <- rep(zero.ah, length(edgeNames(x@map)))

+  names(aHead) <- edgeNames(x@map)

+  aHead[ew > 0] <- pos.ah

+  aHead[ew < 0] <- neg.ah

+  aHead <- aHead[setdiff(seq(along=ew), removedEdges(x@map))]

+  

+  eCol <- rep(zero.col, length(edgeNames(x@map)))

+  names(eCol) <- edgeNames(x@map)

+  eCol[ew > 0] <- pos.col

+  eCol[ew < 0] <- neg.col

+  eCol <- eCol[setdiff(seq(along=ew), removedEdges(x@map))]

+  

+  eStyle <- rep(zero.lty, length(edgeNames(x@map)))

+  names(eStyle) <- edgeNames(x@map)  

+  eStyle[ew > 0] <- pos.lty

+  eStyle[ew < 0] <- neg.lty

+  eStyle <- eStyle[setdiff(seq(along=ew), removedEdges(x@map))]

+  

+  return(list(

+    arrowhead = aHead,

+    col = eCol,

+    lty = eStyle

+  ))

+}

+

+#' Extract node render information from a \code{pePathway} object

+#' 

+#' @param x an object of class \code{\link{pePathway}}

+#' @param y a string representing the factor to be represented (\code{Pert, Acc} or \code{input}; see \code{\link{pePathway}})

+#' @param input.shape shape of nodes that have measured expression change

+#' @param default.shape shape of all other nodes

+#' @param pos.col color of nodes with a positive \code{y} factor

+#' @param neg.col color of nodes with a negative \code{y} factor

+#' @param zero.col color of nodes with the \code{y} factor equal to zero

+#' 

+#' @value a named list as expected by \code{\link{nodeRenderInfo}}

+#' 

+#' @author Calin Voichita and Sorin Draghici

+#' 

+#' @seealso \code{\link{nodeRenderInfo}},\code{\link{par}}

+#' 

+#' @examples

+#' 

+#' # load experiment

+#' load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))

+#' fc <- top$logFC[top$adj.P.Val <= .01]

+#' names(fc) <- top$entrez[top$adj.P.Val <= .01]

+#' ref <- top$entrez

+#' 

+#' # load the set of pathways

+#' kpg <- keggPathwayGraphs("hsa")

+#' kpg <- setEdgeWeights(kpg)

+#' kpg <- setNodeWeights(kpg, defaultWeight = 1)

+#' 

+#' # perform the pathway analysis

+#' peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)

+#' 

+#' p <- peRes@@pathways[[50]]

+#' g <- layoutGraph(p@@map, layoutType = "dot")

+#' graphRenderInfo(g) <- list(fixedsize = FALSE)

+#' edgeRenderInfo(g) <- peEdgeRenderInfo(p)

+#' nodeRenderInfo(g) <- peNodeRenderInfo(p)

+#' # notice the different type of nodes in the graph (box/circle)

+#' # the color of each node represents the perturbation (red = positive, blue = negative)

+#' # the shade represents the stregth of the perturbation 

+#' renderGraph(g)

+#' 

+#' nodeRenderInfo(g) <- peNodeRenderInfo(p, "Acc")

+#' # now, the color of each node represents the accumulation (red = positive, blue = negative)

+#' # notice that square nodes with no parents have no accumulation

+#' renderGraph(g)

+#' 

+#' @export

+peNodeRenderInfo <- function(x, y = "Pert",

+                             input.shape = "box",

+                             default.shape = "ellipse",

+                             pos.col = "red",

+                             neg.col = "blue",

+                             zero.col = "white")

+{

+  stopifnot(class(x) == "pePathway")

+  stopifnot(y %in%  c("input", "Pert", "Acc"))

+  

+  nShape <- rep(default.shape, length(nodes(x@map)))

+  names(nShape) <- nodes(x@map)

+  nShape[names(x@input)] <- input.shape

+  

+  nFillColor <- rep(zero.col, length(nodes(x@map)))

+  names(nFillColor) <- nodes(x@map)

+  pf <- slot(x, y)

+  nFillColor[pf <= 0] <- colorRampPalette(c(zero.col,neg.col))(256)[as.numeric(cut(abs(pf[pf<=0]), 256))]                                  

+  nFillColor[pf >= 0] <- colorRampPalette(c(zero.col,pos.col))(256)[as.numeric(cut(abs(pf[pf>=0]), 256))]

+  

+  return(list(

+    shape = nShape,

+    fill = nFillColor

+  ))

+}

\ No newline at end of file

@@ -1,22 +1,3 @@

-

-#' @keywords internal

-pf2col <- function(pf)

-{

-  retcol <- rep("white", length(pf))

-  

-  ### possitive

-  i <- pf > 0

-  #retcol[i] <- rainbow(256, start = 1/6, end = 2/6)[ceiling(pf[i] / max(pf[i]) * 256)]  

-  retcol[i] <- colorRampPalette(c("white", "red"))(256)[ceiling(pf[i] / max(pf[i]) * 256)]

-  

-  i <- pf < 0

-  #retcol[i] <- rainbow(256, start = 1, end = 1/6)[256:1][ceiling(abs(pf[i]) / max(abs(pf[i])) * 256)]

-  retcol[i] <- colorRampPalette(c("white", "blue"))(256)[ceiling(abs(pf[i]) / max(abs(pf[i])) * 256)]

-  

-  names(retcol) <- names(pf)

-  return(retcol)

-}

-

 #' @keywords internal

 addNames <- function(x, nms)

 {

@@ -33,13 +14,55 @@ addNames <- function(x, nms)

 compute.bootPV <- function(real, dist)

   ( sum(abs(dist - mean(dist)) > abs(real - mean(dist))) + 1 ) / (1 + length(dist))

-#' @keywords internal

-compute.fischer <- function(p)

-  {k <- p[1] * p[2]; return(k-k*log(k))}

+#' Combine independent p-values using the Fischer method

+#' 

+#' @param p a vector of independent p-values

+#' @param eps the minimal p-value considered (all p-values smaller will be set to this value)

+#' 

+#' @value the combined p-value

+#' 

+#' @author Calin Voichita and Sorin Draghici

+#' 

+#' @seealso \code{\link{pe}},\code{\link{compute.normalInv}}

+#' 

+#' @examples

+#' 

+#' p <- c(.1, .01)

+#' compute.fischer(p)

+#' 

+#' @export

+compute.fischer <- function(p, eps = 1e-6)

+{

+  stopifnot(any(p >= 0 & p<=1))  

+  p[p < eps] <- eps

+  

+  k <- prod(p); 

+  return(k-k*log(k))

+}

-#' @keywords internal

-compute.normalInv <- function(p)

-  pnorm( (qnorm(p[1]) + qnorm(p[2])) / sqrt(2) )

+#' Combine independent p-values using the normal inversion method

+#' 

+#' @param p a vector of independent p-values

+#' @param eps the minimal p-value considered (all p-values smaller will be set to this value)

+#' 

+#' @value the combined p-value

+#' 

+#' @author Calin Voichita and Sorin Draghici

+#' 

+#' @seealso \code{\link{pe}},\code{\link{compute.fischer}}

+#' 

+#' @examples

+#' 

+#' p <- c(.1, .01)

+#' compute.normalInv(p)

+#' 

+#' @export

+compute.normalInv <- function(p, eps = 1e-6)

+{

+  stopifnot(any(p >= 0 & p<=1))  

+  p[p < eps] <- eps

+  return(pnorm(sum(sapply(p, qnorm)) / sqrt(length(p))))

+}

 #` @keywords internal

 graph2ftM <- function(g)

similarity index 99%

rename from man/Summary.Rd

rename to man/Summary-methods.Rd

@@ -1,6 +1,6 @@

 \name{Summary}

-\alias{Summary}

 \alias{Summary,peRes-method}

+\alias{Summary.peRes}

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

 \arguments{

   \item{x}{Pathways-Express result object obtained using

new file mode 100644

@@ -0,0 +1,26 @@

+\name{compute.fischer}

+\alias{compute.fischer}

+\title{Combine independent p-values using the Fischer method}

+\usage{

+  compute.fischer(p, eps = 1e-06)

+}

+\arguments{

+  \item{p}{a vector of independent p-values}

+

+  \item{eps}{the minimal p-value considered (all p-values

+  smaller will be set to this value)}

+}

+\description{

+  Combine independent p-values using the Fischer method

+}

+\examples{

+p <- c(.1, .01)

+compute.fischer(p)

+}

+\author{

+  Calin Voichita and Sorin Draghici

+}

+\seealso{

+  \code{\link{pe}},\code{\link{compute.normalInv}}

+}

+

new file mode 100644

@@ -0,0 +1,27 @@

+\name{compute.normalInv}

+\alias{compute.normalInv}

+\title{Combine independent p-values using the normal inversion method}

+\usage{

+  compute.normalInv(p, eps = 1e-06)

+}

+\arguments{

+  \item{p}{a vector of independent p-values}

+

+  \item{eps}{the minimal p-value considered (all p-values

+  smaller will be set to this value)}

+}

+\description{

+  Combine independent p-values using the normal inversion

+  method

+}

+\examples{

+p <- c(.1, .01)

+compute.normalInv(p)

+}

+\author{

+  Calin Voichita and Sorin Draghici

+}

+\seealso{

+  \code{\link{pe}},\code{\link{compute.fischer}}

+}

+

@@ -17,7 +17,7 @@

   \item{nodeOnlyGraphs}{allow graphs with no edges}

-  \item{updateCache}{re-downlaod KEGG data}

+  \item{updateCache}{re-download KEGG data}

   \item{verbose}{show progress of downloading and parsing}

 }

@@ -24,7 +24,7 @@ kpn <- keggPathwayNames("hsa")

 # to update the pathway cache for human run:

 # kpn <- keggPathwayNames("hsa", updateCache = TRUE)

-# this is time consuming and depends on the available bandwith.

+# this is time consuming and depends on the available bandwidth.

 head(kpn)

 }

@@ -1,4 +1,3 @@

-\docType{methods}

 \name{nodeWeights}

 \alias{nodeWeights}

 \alias{nodeWeights,graph,character-method}

@@ -68,6 +67,6 @@ nodeWeights(g, attr = "WT", default = 3)

   Calin Voichita and Sorin Draghici

 }

 \seealso{

-  \link{nodes} \link{nodeData}

+  \link{nodes}, \link{nodeData}

 }

@@ -13,7 +13,7 @@

   \item{graphs}{list of pathway graphs as objects of type

   \code{graph} (e.g., \code{\link{graphNEL}}); the graphs

-  must be weighted graphs (i.e., have an atrribute

+  must be weighted graphs (i.e., have an attribute

   \code{weight} for both nodes and edges)}

   \item{ref}{the reference vector for all genes in the

@@ -118,7 +118,9 @@ head(Summary(peRes))

   17, 2007.

 }

 \seealso{

-  \code{\link{Summary}} \code{\link{keggPathwayGraphs}}

-  \code{\link{setNodeWeights}} \code{\link{setEdgeWeights}}

+  \code{\link{Summary}}, \code{\link{plot.peRes}},

+  \code{\link{keggPathwayGraphs}},

+  \code{\link{setNodeWeights}},

+  \code{\link{setEdgeWeights}}

 }

new file mode 100644

@@ -0,0 +1,68 @@

+\name{peEdgeRenderInfo}

+\alias{peEdgeRenderInfo}

+\title{Extract edge render information from a \code{pePathway} object}

+\usage{

+  peEdgeRenderInfo(x, pos.col = "black", pos.lty = "solid",

+    pos.ah = "vee", neg.col = "black", neg.lty = "dashed",

+    neg.ah = "tee", zero.col = "lightgray",

+    zero.lty = "dotted", zero.ah = "none")

+}

+\arguments{

+  \item{x}{an object of class \code{\link{pePathway}}}

+

+  \item{pos.col}{color of the edges with possitive weight}

+

+  \item{pos.lty}{line type of the edges with possitive

+  weight}

+

+  \item{pos.ah}{arrow head of the edges with possitive

+  weight}

+

+  \item{neg.col}{color of the edges with negative weight}

+

+  \item{neg.lty}{line type of the edges with negative

+  weight}

+

+  \item{neg.ah}{arrow head of the edges with negative

+  weight}

+

+  \item{zero.col}{color of the edges with zero weight}

+

+  \item{zero.lty}{color of the edges with zero weight}

+

+  \item{zero.ah}{color of the edges with zero weight}

+}

+\description{

+  Extract edge render information from a \code{pePathway}

+  object

+}

+\examples{

+# load experiment

+load(system.file("extdata/E-GEOD-21942.topTable.RData", package = "ROntoTools"))

+fc <- top$logFC[top$adj.P.Val <= .01]

+names(fc) <- top$entrez[top$adj.P.Val <= .01]

+ref <- top$entrez

+

+# load the set of pathways

+kpg <- keggPathwayGraphs("hsa")

+kpg <- setEdgeWeights(kpg)

+kpg <- setNodeWeights(kpg, defaultWeight = 1)

+

+# perform the pathway analysis

+peRes <- pe(fc, graphs = kpg, ref = ref, nboot = 100, verbose = TRUE)

+

+p <- peRes@pathways[[50]]

+g <- layoutGraph(p@map, layoutType = "dot")

+graphRenderInfo(g) <- list(fixedsize = FALSE)

+edgeRenderInfo(g) <- peEdgeRenderInfo(p)

+nodeRenderInfo(g) <- peNodeRenderInfo(p)

+# notice the different type of edges in the graph (solid/dashed/dotted)

+renderGraph(g)

+}

+\author{

+  Calin Voichita and Sorin Draghici

+}