@@ -1,13 +1,11 @@

 Package: rTRM

 Type: Package

-Title: Identification of transcriptional regulatory modules

-Version: 0.9.7

-Date: 2013-06-16

+Title: Identification of transcriptional regulatory modules from PPI networks

+Version: 0.99.0

+Date: 2013-07-25

 Author: Diego Diez

 Depends: R (>= 2.10), igraph, RSQLite

-Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt,

-        knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8, org.Mm.eg.db,

-        AnnotationDbi, annotate

+Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8, org.Mm.eg.db, AnnotationDbi, annotate

 Maintainer: Diego Diez <[email protected]>

 Description: rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.

 License: GPL-3

@@ -99,3 +99,62 @@ getConcentricList = function(g, t, e, max.size = 60, order.by = "label") {

 	}

 	res

 }

+

+layout.arc = function (g, target, query)

+{

+  n = vcount(g)

+  if(! all(target %in% V(g)$name)) {

+    warning("some targets not in graph, removing them.")

+    target=target[target %in% V(g)$name]

+  }

+  

+  #

+  target = target[target %in% query]

+  

+  V(g)$type = "bridge"

+  V(g)[name %in% query]$type = "query"

+  V(g)[name %in% target]$type = "target"

+  

+  g_con = g

+  n_left = character()

+  

+  if(! is.connected(g)) {

+    g_con = getLargestComp(g)

+    n_left = setdiff(V(g)$name,V(g_con)$name)

+  }

+  

+  set = list(target = target, bridge=V(g_con)[type == "bridge"]$name, query1 = character(), query2 = character(), query3 = character(), left=n_left)

+  for(q in V(g_con)[type == "query"]$name) {

+    sp = get.all.shortest.paths(g_con,from=V(g_con)[q],to=V(g_con)[name %in% target])

+    print(sp)

+    sp_min = min(sapply(sp$res,length))

+    print(sp_min)

+    if(sp_min == 2) {

+      set$query1 = c(set$query1, V(g_con)[q]$name)

+    }

+    else set$query2 = c(set$query2, V(g_con)[q]$name)

+  }

+  

+  set = lapply(set,function(s) {

+    ns = V(g)[s]$label

+    s[order(ns,decreasing=TRUE)]

+  })

+  

+  x0 = c(left=-2,query1=-1,target=0,bridge=1,query2=2)

+  y0 = sapply(set,function(x){

+    -1 * floor(length(x)/2)

+  })

+  

+  res = matrix(NA, nrow = n, ncol = 2)

+  all_n = unlist(set)

+  for(my_n in all_n) {

+    k = which(V(g)$name == my_n)

+    my_type = names(set)[sapply(set,function(x) my_n %in% x)]

+    x1 = x0[my_type]

+    y1 = y0[my_type]

+    y0[my_type] = y0[my_type] + 1

+    res[k,1] = x1

+    res[k,2] = y1

+  }

+  res

+}

\ No newline at end of file

@@ -137,7 +137,7 @@ annotateTRM = function(g, target) {

     default

 }

-plotTRM = function(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, label.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = FALSE) {

+plotTRM = function(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, label.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = FALSE, normalizr.layout=TRUE) {

   if(class(layout) == "function")

     l = layout(g)

@@ -145,7 +145,8 @@ plotTRM = function(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col

     l = layout

   # normalize layout.

-  l = layout.norm(l, -1, 1, -1, 1)

+  if(normalize.layout)

+    l = layout.norm(l, -1, 1, -1, 1)

   vertex.col = .checkParam(vertex.col, V(g)$frame.color, "black", multi = vcount(g))

   vertex.cex = .checkParam(vertex.cex, V(g)$size, 10, multi = vcount(g))

@@ -238,14 +239,15 @@ plotTRMlegend = function (x, title = NULL, cex = 1)

     symbols(xpos, ypos, circles = radius, inches = FALSE, add = TRUE, fg = frame.color, lwd = frame.width)

 }

-plotGraph = function(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offset = 1.5, adjust.label.col = FALSE) { 

+plotGraph = function(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offset = 1.5, adjust.label.col = FALSE, normalize.layout=TRUE) { 

   if(class(layout) == "function")

     l = layout(g)

   else

     l = layout

   # normalize layout.

-  l = layout.norm(l, -1, 1, -1, 1)

+  if(normalize.layout)

+    l = layout.norm(l, -1, 1, -1, 1)

   vertex.cex = .checkParam(vertex.cex, V(g)$size, 5)

   vertex.col = .checkParam(vertex.col, V(g)$frame.color, "grey")

Binary files a/data/biogrid_hs.rda and b/data/biogrid_hs.rda differ

Binary files a/data/biogrid_mm.rda and b/data/biogrid_mm.rda differ

@@ -8,7 +8,7 @@ Plot an graph in igraph format.

 This function plots graphs of the class igraph.

 }

 \usage{

-plotGraph(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offset = 1.5, adjust.label.col = FALSE)

+plotGraph(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, vertex.cex, vertex.col, vertex.bg, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, label.col, label.cex, label.pos = NULL, label.offset = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE)

 }

 %- maybe also 'usage' for other objects documented here.

 \arguments{

@@ -33,9 +33,8 @@ plotGraph(g, layout = layout.fruchterman.reingold, mar = .5, vertex.pch = 21, ve

   \item{label.offset}{label offset.}

   \item{adjust.label.col}{

-whether to automatically adjust label color depending on the luminance of the node's color/s.

-

-}

+whether to automatically adjust label color depending on the luminance of the node's color/s.}

+  \item{normalize.layout}{whether to apply layout.norm (with limits xmin=-1, xmax=1, ymin=-1, ymax=1) to the layout.}

 }

 \author{

@@ -8,7 +8,7 @@ Plot an annotated TRM.

 This function plots the output findTRM() after it has been annotated with cluster information with annotateTRM() function. Cluster membership is plotted using a pie plot.

 }

 \usage{

-plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, label.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = FALSE)

+plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col, vertex.cex, vertex.lwd, edge.col, edge.lwd, edge.lty, label = TRUE, label.cex, label.col, label.pos = NULL, label.offset = 1.5, adjust.label.col = FALSE, normalize.layout = TRUE)

 }

 %- maybe also 'usage' for other objects documented here.

 \arguments{

@@ -30,6 +30,7 @@ plotTRM(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col, vertex.ce

   \item{label.pos}{label position.}

   \item{label.offset}{label offset.}

   \item{adjust.label.col}{whether to automatically adjust label color depending on the luminance of the node's color.}

+  \item{normalize.layout}{whether to apply layout.norm (with limits xmin=-1, xmax=1, ymin=-1, ymax=1) to the layout.}

 }

 \author{

@@ -6,10 +6,7 @@

 	Identification transcription regulatory modules (TRMs)

 }

 \description{

-	This package integrates transcription factor binding, enrichment analysis,

-	gene expression, functional information  and protein-protein interaction

-	data, and identifies transcription factor modules (TFM) that regulate

-	cellular responses.

+	This package identifies transcriptional regulatory modules (TRMs) from PPI networks.

 }

 \details{

 \tabular{ll}{