@@ -137,13 +137,12 @@ annotateTRM = function(g, target) {

   else

     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, normalize.layout=TRUE) {

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

+  if(is(layout, "function"))

     l = layout(g)

   else

-    l = layout

+    l = as.matrix(layout)

   # normalize layout.

   if(normalize.layout)

@@ -320,14 +320,14 @@ annotateModule = function(g, enrich, trm, targets, ppi, exprs, tfs) {

 	}

 	E(g)$lty = "dotted"

-	el = get.edgelist(graph.intersection.by.name(ppi, g))

+	el = get.edgelist(graph.intersection(ppi, g))

 	for(j in 1:nrow(el)) {

 		E(g, P = which(V(g)$name %in% el[j,]), directed = FALSE)$lty = "solid"

 	}

 	E(g)$color = "grey"

 	E(g)$width = 1

-	el = get.edgelist(graph.intersection.by.name(trm, g))

+	el = get.edgelist(graph.intersection(trm, g))

 	for(j in 1:nrow(el)) {

 		E(g, P = which(V(g)$name %in% el[j,]), directed = FALSE)$color = "black"

 		#		E(g, P = which(V(g)$name %in% el[j,]), directed = FALSE)$width = 3

@@ -105,7 +105,8 @@ plotDegree = function(g) {

   V(g)$family = family

   col = c("unclassified" = "white", .getTFclassColors())

-  V(g)$piecolor = lapply(V(g)$family, function(f) col[f])

+  V(g)$pie.color = lapply(V(g)$family, function(f) col[f])

+  V(g)$pie = lapply(V(g)$pie.color, function(f) rep(1,length(f)))

   g

 }

@@ -161,7 +162,7 @@ plotTRM = function(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col

   if (adjust.label.col) {

     col.range = range(.lum2(colors()))

     col.cut = round(diff(col.range)/2)

-    lum.mean = sapply(V(g)$piecolor, function(x) mean(.lum2(x)))

+    lum.mean = sapply(V(g)$pie.color, function(x) mean(.lum2(x)))

     label.col = ifelse(lum.mean < col.cut, "snow", "gray20")

   }

@@ -176,8 +177,9 @@ plotTRM = function(g, layout = layout.fruchterman.reingold, mar = .5, vertex.col

     lines(c(x1[1], x2[1]), c(x1[2], x2[2]), col = edge.col, lwd = edge.lwd[i], lty = edge.lty[i])

   }

   for(i in 1:nrow(l)) {

-    np = rep(1, length(V(g)[ i ]$piecolor))

-    .floating.pie(l[i,1], l[i,2], x = np, col = V(g)[ i ]$piecolor, radius=vertex.cex[i]/100, frame.width = vertex.lwd[i], frame.color = vertex.col[i])

+    np=V(g)$pie[[i]]

+    col=V(g)$pie.color[[i]]

+    .floating.pie(l[i,1], l[i,2], x=np, col=col, radius=vertex.cex[i]/100, frame.width=vertex.lwd[i], frame.color=vertex.col[i])

   }

   if(label) {

     ll = as.character(V(g))

@@ -218,7 +220,7 @@ plotTRMlegend = function (x, title = NULL, cex = 1)

   if (!is.null(col)) 

     col <- rep(col, length.out = nx)

-  

+    

   if (!is.null(lty)) 

     lty <- rep(lty, length.out = nx)

@@ -263,7 +265,7 @@ plotGraph = function(g, layout = layout.fruchterman.reingold, mar = .5, vertex.p

   if (adjust.label.col) {

     col.range = range(.lum2(colors()))

     col.cut = round(diff(col.range)/2)

-    lum.mean = sapply(V(g)$piecolor, function(x) mean(.lum2(x)))

+    lum.mean = sapply(V(g)$pie.color, function(x) mean(.lum2(x)))

     label.col = ifelse(lum.mean < col.cut, "snow", "gray20")

   }

@@ -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, normalizr.layout=TRUE) {

+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, normalize.layout=TRUE) {

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

     l = layout(g)

@@ -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")

new file mode 100644

@@ -0,0 +1,368 @@

+## Package: rTRM (c)

+##

+## File: plot.R

+## Description: support plotting functions for rTRM

+##

+## Author: Diego Diez

+## Contact: [email protected]

+##

+

+

+## plots the degree distribution of the graph object.

+plotDegree = function(g) {

+	d = table(igraph::degree(g))

+	x = as.numeric(names(d))

+	y = as.numeric(d)

+		

+	x0 = x[! x == 0 ]

+	y0 = y[! x == 0 ]

+	

+	plot(x0, y0, log = "xy", xlab = "Degree", ylab = "# Nodes", pch = 21, bg = "gray")

+	

+	dl = lm(log10(y0) ~ log10(x0))

+	abline(dl)

+	l = .getLegend(dl)

+	legend("topright", l, bg = "white", lty = "solid", cex = 0.7)

+}

+

+.getLegend <- function(m) {

+	s <- summary(m)

+	r2 = format(s$r.squared, nsmall = 2, digits = 2)

+	a = format(m$coef[1], nsmall = 2, digits = 2)

+	if (m$coef[2] > 0) {

+		b = format(m$coef[2], nsmall = 2, digits = 2)

+		l <- eval(substitute(expression(paste(R^2 == r2, 

+			", ", y == a + b * x)), list(r2 = r2, a = a, 

+			b = b)))

+	}

+	else {

+		b = format(abs(m$coef[2]), nsmall = 2, digits = 2)

+		l <- eval(substitute(expression(paste(r^2 == r2, 

+			", ", y == a - b * x)), list(r2 = r2, a = a, 

+			b = b)))

+	}

+}

+

+

+.lum = function(col) {

+    tmp = col2rgb(col)

+    apply(tmp, 2, function(x) {

+    (0.2126*x[1]) + (0.7152*x[2]) + (0.0722*x[3])

+    })

+}

+

+

+.lum2 = function (col) 

+{

+    tmp = col2rgb(col)

+    apply(tmp, 2, function(x) {

+        (0.2126 * x[1]^2) + (0.7152 * x[2]^2) + (0.0722 * x[3]^2)

+    })

+}

+

+

+.getNiceColors = function (n, eq.spaced = TRUE, order.by = TRUE, min.lum, max.lum) 

+{

+    cs = grep("^grey|^gray", colors(), value = TRUE, invert = TRUE)

+    cs = grep("white", cs, value = TRUE, invert = TRUE)

+    cols = c(cs, grey.colors(10))

+  

+    cols.lum = .lum2(cols)

+      

+    if (order.by) {

+    	#cols.lum = lum2(cols)

+      sel = order(cols.lum, decreasing = TRUE)

+      cols = cols[sel]

+      cols.lum = cols.lum[sel]

+    }

+    

+    if(!missing(min.lum))

+    	cols = cols[cols.lum >= min.lum]

+    

+    if(!missing(max.lum))

+    	cols = cols[cols.lum <= max.lum]

+    

+    if(!missing(n)) {

+    	if(eq.spaced) {

+	    	ns = floor(length(cols)/n)

+    		sel = seq(1, ns * n, ns)

+    		cols = cols[sel]

+    	} else cols = cols[1:n]

+    }

+    cols

+}

+

+.getTFclassColors = function(subset = "Class") {

+  terms = getTFterms(subset)

+  col = .getNiceColors(length(unique(terms)))

+  names(col) = unique(terms)

+  col

+}

+

+.annotateTFclass = function(g) {

+  family = getTFclassFromEntrezgene(V(g)$name)

+  family[sapply(family, is.null)] = "unclassified"

+  V(g)$family = family

+  

+  col = c("unclassified" = "white", .getTFclassColors())

+  V(g)$piecolor = lapply(V(g)$family, function(f) col[f])

+  g

+}

+

+.annotateTarget = function(g, target) {

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

+  V(g)$frame.color = "grey"

+  V(g)[ target ]$frame.color = "black"

+  V(g)$frame.width = 1

+  V(g)[ target ]$frame.width = 2

+  g

+}

+

+annotateTRM = function(g, target) {

+  g = .annotateTarget(g, target)

+  .annotateTFclass(g)

+}

+

+.checkParam = function(p1, p2, default, multi) {

+  if(!missing(p1))

+    if(!missing(multi) & length(p1) == 1)

+      return(rep(p1, multi))

+  else

+    return(p1)

+  if(!is.null(p2))

+    return(p2)

+  if(!missing(multi))

+    rep(default, multi)

+  else

+    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) {

+  

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

+    l = layout(g)

+  else

+    l = layout

+

+  # 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))

+  vertex.lwd = .checkParam(vertex.lwd, V(g)$frame.width, 1, multi = vcount(g))

+  

+  edge.col = .checkParam(edge.col, E(g)$color, "grey")

+  edge.lwd = .checkParam(edge.lwd, E(g)$width, 1, multi = ecount(g))

+  edge.lty = .checkParam(edge.lty, E(g)$lty, "solid", multi = ecount(g))

+  

+  label.col = .checkParam(label.col, V(g)$label.color, "black")

+  label.cex = .checkParam(label.cex, V(g)$label.cex, 1)

+  if (adjust.label.col) {

+    col.range = range(.lum2(colors()))

+    col.cut = round(diff(col.range)/2)

+    lum.mean = sapply(V(g)$piecolor, function(x) mean(.lum2(x)))

+    label.col = ifelse(lum.mean < col.cut, "snow", "gray20")

+  }

+  

+  mat = get.edgelist(g)

+  

+  op = par(mar = rep(mar,4), xpd = TRUE)

+  plot(0, xlim = range(l[,1]), ylim = range(l[,2]), cex = 0, axes = FALSE, xlab = "", ylab = "", asp = 1)

+  for(i in 1:nrow(mat)){

+    ni = as.numeric(V(g)[ mat[i,] ])

+    x1 = l[ni[1] ,]

+    x2 = l[ni[2] ,]

+    lines(c(x1[1], x2[1]), c(x1[2], x2[2]), col = edge.col, lwd = edge.lwd[i], lty = edge.lty[i])

+  }

+  for(i in 1:nrow(l)) {

+    np = rep(1, length(V(g)[ i ]$piecolor))

+    .floating.pie(l[i,1], l[i,2], x = np, col = V(g)[ i ]$piecolor, radius=vertex.cex[i]/100, frame.width = vertex.lwd[i], frame.color = vertex.col[i])

+  }

+  if(label) {

+    ll = as.character(V(g))

+    if(!is.null(V(g)$name))

+      ll = V(g)$name

+    if(!is.null(V(g)$label))

+      ll = V(g)$label

+    text(l, labels = ll, cex = label.cex, col = label.col, pos = label.pos, offset = label.offset) 

+  }

+  par(op)

+}

+

+plotTRMlegend = function (x, title = NULL, cex = 1) 

+{

+	

+	if(class(x) == "igraph")

+  	family = sort(unique(unlist(V(x)$family)))

+	else

+		family = x

+  

+  col = .getTFclassColors()

+  col = c(col, unclassified = "white")

+  

+  op = par(mar = rep(0, 4))

+  plot(0, col = "transparent", axes = FALSE)

+  legend("center", legend = family, fill = col[family], bty = "n", cex = cex, title = title)

+  par(op)

+}

+

+.floating.pie = function (xpos, ypos, x, edges = 200, radius = 0.8, col = NULL, border = TRUE, lty = NULL, frame.color = "black", frame.width = 1)

+{

+  if (!is.numeric(x) || any(is.na(x) | x < 0)) 

+    stop("'x' values must be positive.")

+  

+  x <- c(0, cumsum(x)/sum(x))

+  dx <- diff(x)

+  nx <- length(dx)

+  

+  if (!is.null(col)) 

+    col <- rep(col, length.out = nx)

+  

+  if (!is.null(lty)) 

+    lty <- rep(lty, length.out = nx)

+  

+  

+  init.angle = 90

+  

+  t2xy = function(t) {

+    t2p <- -2 * pi * t + init.angle * pi/180

+    list(x = radius * cos(t2p), y = radius * sin(t2p))

+  }

+  

+  for (i in 1L:nx) {

+    n <- max(2, floor(edges * dx[i]))

+    P <- t2xy(seq.int(x[i], x[i + 1], length.out = n))

+    polygon(c(P$x+xpos, xpos), c(P$y+ypos, ypos), border = NA, col = col[i], lty = lty[i])

+  }

+  if (border) 

+    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) { 

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

+    l = layout(g)

+  else

+    l = layout

+  

+  # 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")

+  vertex.bg = .checkParam(vertex.bg, V(g)$color, "white")

+  vertex.lwd = .checkParam(vertex.lwd, V(g)$frame.width, 1)

+  

+  edge.col = .checkParam(edge.col, E(g)$color, "grey", multi = ecount(g))

+  edge.lwd = .checkParam(edge.lwd, E(g)$width, 1, multi = ecount(g))

+  edge.lty = .checkParam(edge.lty, E(g)$lty, "solid", multi = ecount(g))

+  

+  label.col = .checkParam(label.col, V(g)$label.color, "black")

+  label.cex = .checkParam(label.cex, V(g)$label.cex, 1)

+  if (adjust.label.col) {

+    col.range = range(.lum2(colors()))

+    col.cut = round(diff(col.range)/2)

+    lum.mean = sapply(V(g)$piecolor, function(x) mean(.lum2(x)))

+    label.col = ifelse(lum.mean < col.cut, "snow", "gray20")

+  }

+  

+  mat = get.edgelist(g)

+  op = par(mar = rep(mar,4), xpd = TRUE)

+  plot(0, xlim = range(l[,1]), ylim = range(l[,2]), cex = 0, axes = FALSE, xlab = "", ylab = "", asp = 1)

+  for(i in 1:nrow(mat)){

+    ni = as.numeric(V(g)[ mat[i,] ])

+    x1 = l[ni[1] ,]

+    x2 = l[ni[2] ,]

+    lines(c(x1[1], x2[1]), c(x1[2], x2[2]), col = edge.col[i], lwd = edge.lwd[i], lty = edge.lty[i])

+  }

+  points(l, pch = vertex.pch, cex = vertex.cex, bg = vertex.bg, col = vertex.col, lwd = vertex.lwd)

+  if(label) {

+    ll = as.character(V(g))

+    if(!is.null(V(g)$name))

+      ll = V(g)$name

+    if(!is.null(V(g)$label))

+      ll = V(g)$label

+    text(l, labels = ll, cex = label.cex, pos = label.pos, offset=label.offset) 

+  }

+  par(op)

+}

+

+

+## annotation functions to compare modules.

+# annotate a graph based on the information in other module, as well as expression and targets, etc.

+annotateModule = function(g, enrich, trm, targets, ppi, exprs, tfs) {

+  trm_genes = .checkInNetwork(g, V(trm)$name)

+  enrich_genes = .checkInNetwork(g, enrich)

+  targets_found = targets[targets %in% trm]

+  targets_found = .checkInNetwork(g, targets_found)

+  exprs = .checkInNetwork(g, exprs)

+                             

+	V(g)$color = "white"

+	V(g)[ trm_genes ]$color = "white"

+	V(g)[ enrich_genes ]$color = "steelblue2"

+	

+	V(g)[ targets_found ]$color = "steelblue4"

+	V(g)$size = 1

+	V(g)[ exprs ]$size = 15

+	

+	V(g)$frame.color = "gray"

+	V(g)$frame.width = 1

+	V(g)[ trm_genes ]$frame.color = "black"

+	V(g)[ trm_genes ]$frame.width = 3

+		

+	if(!missing(tfs)) {

+	  tfs = .checkInNetwork(g, tfs)

+		V(g)$shape = "circle"

+		V(g)[ tfs ]$shape = "square"

+	}

+	

+	E(g)$lty = "dotted"

+	el = get.edgelist(graph.intersection.by.name(ppi, g))

+	for(j in 1:nrow(el)) {

+		E(g, P = which(V(g)$name %in% el[j,]), directed = FALSE)$lty = "solid"

+	}

+	

+	E(g)$color = "grey"

+	E(g)$width = 1

+	el = get.edgelist(graph.intersection.by.name(trm, g))

+	for(j in 1:nrow(el)) {

+		E(g, P = which(V(g)$name %in% el[j,]), directed = FALSE)$color = "black"

+		#		E(g, P = which(V(g)$name %in% el[j,]), directed = FALSE)$width = 3

+	}

+	

+	g

+}

+

+

+# annotate a graph based on the frequency the nodes and edges appear in 

+# a set of other graphs, provided as graph_list.

+annotateFreq = function(g, graph_list) {

+	s = sapply(V(g)$name, function(x) {

+		10*length(which(sapply(graph_list, function(s) if(!is.null(s)) any(V(s)$name %in% x) else FALSE)))/length(graph_list[!sapply(graph_list, is.null)])

+	})

+	

+	ew = apply(get.edgelist(g), 1, function(e) {

+		sum(sapply(names(graph_list), function(n) {

+

+			s = graph_list[[n]]

+			if(!is.null(s)) {

+        e = .checkInNetwork(s, e)

+				if(length(V(s)[ e ]) == 2)

+					if(are.connected(s, e[1], e[2])) return(1)

+			}

+			return(0)

+		}))

+	})

+	

+	et = rep("solid", length(ew))

+	et[ew == 0] = "dotted"

+	ew[ew == 0] = 1

+	

+	V(g)$size = s

+	E(g)$width = ew

+	E(g)$lty = et

+	g

+}

+

+.checkInNetwork = function(g, x) {

+  x[ x %in% V(g)$name ]

+}