1. ComplexHeatmap
  2. Commit 451e6d73bc6291dddb32c99dbe51695e44ee82f8
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 25191b4dc0bd4242c260ef5abd112d4bdd0ea887

add oncoPrint() function



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107561 bc3139a8-67e5-0310-9ffc-ced21a209358

z.gu authored on 18/08/2015 22:21:59
Showing 19 changed files
.travis.yml
History View file @ 451e6d7
... ... 
@@ -16,5 +16,6 @@ r-packages:
16 16
17 17 
 r_github_packages:
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 - jokergoo/circlize
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+- jokergoo/HilbertCurve
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 r_check_args: --no-build-vignettes --no-vignettes
DESCRIPTION
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... ... 
@@ -2,13 +2,14 @@ Package: ComplexHeatmap
2 2 
 Type: Package
3 3 
 Title: Making Complex Heatmaps
4 4 
 Version: 1.3.0
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-Date: 2015-8-6
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+Date: 2015-8-18
6 6 
 Author: Zuguang Gu
7 7 
 Maintainer: Zuguang Gu <z.gu@dkfz.de>
8 8 
 Depends: R (>= 3.1.2), grid, graphics, stats, grDevices
9 9 
 Imports: methods, circlize (>= 0.3.1), GetoptLong, colorspace,
10 10 
     RColorBrewer, dendextend (>= 1.0.1), GlobalOptions (>= 0.0.6)
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-Suggests: testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust, dendsort
11 
+Suggests: testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust,
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+    dendsort, HilbertCurve (>= 0.99.2)
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 VignetteBuilder: knitr
13 14 
 Description: Complex heatmaps are efficient to visualize associations
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     between different sources of data sets and reveal potential structures.
... ... 
@@ -17,6 +18,6 @@ Description: Complex heatmaps are efficient to visualize associations
17 18 
 biocViews: Software, Visualization, Sequencing
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 URL: https://github.com/jokergoo/ComplexHeatmap
19 20 
 License: GPL (>= 2)
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-Packaged: 2015-8-6 00:00:00 UTC; Administrator
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+Packaged: 2015-8-18 00:00:00 UTC; Administrator
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 Repository: Bioconductor
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-Date/Publication: 2015-8-6 00:00:00
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+Date/Publication: 2015-8-18 00:00:00
NAMESPACE
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... ... 
@@ -22,6 +22,7 @@ export(decorate_column_hclust)
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 exportMethods(draw_hclust)
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 exportClasses(SingleAnnotation)
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 export(SingleAnnotation)
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+export(oncoPrint)
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 exportClasses(AdditiveUnit)
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 export(AdditiveUnit)
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 export(max_text_height)
NEWS
History View file @ 451e6d7
... ... 
@@ -8,6 +8,7 @@ CHANGES in VERSION 1.3.0
8 8 
 * change default colors for matrix
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 * allow heatmap with zero-row
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 * heatmap components can all have absolute units
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+* add `oncoPriint()`
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12 13 
 =========================================
13 14
R/Heatmap-class.R
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... ... 
@@ -117,6 +117,8 @@ Heatmap = setClass("Heatmap",
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 # -name name of the heatmap. The name is used as the title of the heatmap legend.
118 118 
 # -na_col color for ``NA`` values.
119 119 
 # -rect_gp graphic parameters for drawing rectangles (for heatmap body).
120 
+# -color_space the color space in which colors are interpolated. Only used if ``matrix`` is numeric and
121 
+#            ``col`` is a vector of colors. Pass to `circlize::colorRamp2`.
120 122 
 # -cell_fun self-defined function to add graphics on each cell. Seven parameters will be passed into
121 123 
 #           this function: ``i``, ``j``, ``x``, ``y``, ``width``, ``height``, ``fill`` which are row index,
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 #           column index in ``matrix``, coordinate of the middle points in the heatmap body viewport,
... ... 
@@ -204,8 +206,8 @@ Heatmap = setClass("Heatmap",
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 # == author
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 # Zuguang Gu <z.gu@dkfz.de>
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 #
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-Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),
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-    cell_fun = function(j, i, x, y, width, height, fill) NULL,
209 
+Heatmap = function(matrix, col, name, na_col = "grey", color_space = "LAB",
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+    rect_gp = gpar(col = NA), cell_fun = function(j, i, x, y, width, height, fill) NULL,
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     row_title = character(0), row_title_side = c("left", "right"),
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     row_title_gp = gpar(fontsize = 14),
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     row_title_rot = switch(row_title_side[1], "left" = 90, "right" = 270),
... ... 
@@ -377,7 +379,7 @@ Heatmap = function(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),
377 379 
                     .Object@matrix_color_mapping = ColorMapping(colors = col, name = name, na_col = na_col)
378 380 
                 } else if(is.numeric(matrix)) {
379 381 
                     col = colorRamp2(seq(min(matrix, na.rm = TRUE), max(matrix, na.rm = TRUE), length = length(col)),
380 
-                                     col)
382 
+                                     col, space = color_space)
381 383 
                     .Object@matrix_color_mapping = ColorMapping(col_fun = col, name = name, na_col = na_col)
382 384 
                 } else {
383 385 
                     stop("`col` should have names to map to values in `mat`.")
R/densityHeatmap.R
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... ... 
@@ -5,6 +5,7 @@
5 5 
 # == param
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 # -data  a matrix or a list. If it is a matrix, density will be calculated by columns.
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 # -col a list of colors that density values are scaled to.
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+# -color_space the color space in which colors are interpolated. Pass to `circlize::colorRamp2`.
8 9 
 # -anno annotation for matrix columns or list. The value should be a vector or a data frame.
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 #       It can also be a `HeatmapAnnotation-class` object.
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 # -ylab label on y-axis in the plot
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@@ -31,7 +32,7 @@
31 32 
 # densityHeatmap(lt)
32 33 
 #
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 densityHeatmap = function(data, col = rev(brewer.pal(11, "Spectral")),
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-	anno = NULL, ylab = deparse(substitute(data)),
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+	color_space = "RGB", anno = NULL, ylab = deparse(substitute(data)),
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 	title = paste0("Density heatmap of ", deparse(substitute(data)))) {
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37 38 
 	if(is.matrix(data)) {
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@@ -62,13 +63,13 @@ densityHeatmap = function(data, col = rev(brewer.pal(11, "Spectral")),
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 	colnames(mat) = nm
63 64
64 65 
 	if(is.null(anno)) {
65 
-		ht = Heatmap(mat, col = col, name = "density", cluster_rows = FALSE, cluster_columns = FALSE)
66 
+		ht = Heatmap(mat, col = col, color_space = color_space, name = "density", cluster_rows = FALSE, cluster_columns = FALSE)
66 67 
 	} else if(inherits(anno, "HeatmapAnnotation")) {
67 
-		ht = Heatmap(mat, col = col, top_annotation = anno, name = "density", cluster_rows = FALSE, cluster_columns = FALSE)
68 
+		ht = Heatmap(mat, col = col, color_space = color_space, top_annotation = anno, name = "density", cluster_rows = FALSE, cluster_columns = FALSE)
68 69 
 	} else {
69 70 
 		if(!is.data.frame(anno)) anno = data.frame(anno = anno)
70 71 
 		ha = HeatmapAnnotation(df = anno)
71 
-		ht = Heatmap(mat, col = col, top_annotation = ha, name = "density", cluster_rows = FALSE, cluster_columns = FALSE)
72 
+		ht = Heatmap(mat, col = col, color_space = color_space, top_annotation = ha, name = "density", cluster_rows = FALSE, cluster_columns = FALSE)
72 73 
 	}
73 74
74 75 
 	bb = grid.pretty(c(min_x, max_x))
R/oncoPrint.R
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new file mode 100644
... ... 
@@ -0,0 +1,196 @@
1 
+
2 
+# == title
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+# Make oncoPrint
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+#
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+# == param
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+# -mat a character matrix which encodes mulitple alterations or a list of matrix for which every matrix contains binary
7 
+#      value representing the alteration is present or absent. When it is a list, the names represent alteration types.
8 
+# -get_type If different alterations are encoded in the matrix, this self-defined function
9 
+#           determines how to extract them. Only work when ``mat`` is a matrix.
10 
+# -alter_fun_list a list of functions which define how to add graphics for different alterations.
11 
+#                 The names of the list should cover all alteration types.
12 
+# -col a vector of color for which names correspond to alteration types.
13 
+# -show_column_names whether show column names
14 
+# -pct_gp graphic paramters for percent row annotation
15 
+# -axis_gp graphic paramters for axes
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+# -show_row_barplot whether show barplot annotation on rows
17 
+# -row_barplot_width width of barplot annotation on rows. It should be a `grid::unit` object
18 
+# -show_column_barplot whether show barplot annotation on columns
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+# -column_barplot_height height of barplot annotatioin on columns. it should be a `grid::unit` object.
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+# -... pass to `Heatmap`
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+#
22 
+# == details
23 
+# The function returns a normal heatmap list and you can add more heatmaps/row annotations to it.
24 
+#
25 
+# For more explanation, please go to the vignette.
26 
+#
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+# == value
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+# a `HeatmapList-class` object.
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+#
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+# == author
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+# Zuguang Gu <z.gu@dkfz.de>
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+#
33 
+oncoPrint = function(mat, get_type = function(x) x,
34 
+	alter_fun_list, col, show_column_names = FALSE,
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+	pct_gp = gpar(), axis_gp = gpar(fontsize = 8),
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+	show_row_barplot = TRUE, row_barplot_width = unit(2, "cm"),
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+	show_column_barplot = TRUE, column_barplot_height = unit(2, "cm"),
38 
+	...) {
39 
+
40 
+	# convert mat to mat_list
41 
+	if(inherits(mat, "matrix")) {
42 
+
43 
+		all_type = unique(unlist(lapply(mat, get_type)))
44 
+		all_type = all_type[!is.na(all_type)]
45 
+		all_type = all_type[grepl("\\S", all_type)]
46 
+
47 
+		mat_list = lapply(all_type, function(type) {
48 
+			m = sapply(mat, function(x) type %in% get_type(x))
49 
+			dim(m) = dim(mat)
50 
+			dimnames(m) = dimnames(mat)
51 
+			m
52 
+		})
53 
+	} else if(inherits(mat, "list")) {
54 
+		mat_list = mat
55 
+		all_type = names(mat_list)
56 
+		mat_list = lapply(mat_list, function(x) {
57 
+				oattr = attributes(x)
58 
+				x = as.logical(x)
59 
+				attributes(x) = oattr
60 
+				x
61 
+			})
62 
+
63 
+		if(length(unique(sapply(mat_list, nrow))) > 1) {
64 
+			stop("All matrix in 'mat_list' should have same number of rows.")
65 
+		}
66 
+
67 
+		if(length(unique(sapply(mat_list, ncol))) > 1) {
68 
+			stop("All matrix in 'mat_list' should have same number of columns.")
69 
+		}
70 
+	} else {
71 
+		stop("Incorrect type of 'mat'")
72 
+	}
73 
+
74 
+	# type as the third dimension
75 
+	arr = array(FALSE, dim = c(dim(mat_list[[1]]), length(all_type)), dimnames = c(dimnames(mat_list[[1]]), list(all_type)))
76 
+	for(i in seq_along(all_type)) {
77 
+		arr[, , i] = mat_list[[i]]
78 
+	}
79 
+
80 
+	l = rowSums(apply(arr, c(2, 3), sum)) > 0
81 
+	arr = arr[, l, , drop = FALSE]
82 
+
83 
+	# validate alter_fun_list
84 
+	if(is.null(alter_fun_list$background)) alter_fun_list$background = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "#CCCCCC", col = NA))
85 
+	sdf = setdiff(all_type, names(alter_fun_list))
86 
+	if(length(sdf) > 0) {
87 
+		stop(paste0("You should define shape function for:", paste(sdf, collapse = ", ")))
88 
+	}
89 
+
90 
+	all_type = names(alter_fun_list)
91 
+	all_type = setdiff(all_type, "background")
92 
+
93 
+	arr = arr[, , all_type, drop = FALSE]
94 
+
95 
+	# validate col
96 
+	sdf = setdiff(all_type, names(col))
97 
+	if(length(sdf) > 0) {
98 
+		stop(paste0("You should define colors for:", paste(sdf, collapse = ", ")))
99 
+	}
100 
+
101 
+	add_oncoprint = function(type, x, y, width, height) {
102 
+		alter_fun_list[[type]](x, y, width, height)
103 
+	}
104 
+
105 
+	# for each gene, percent of samples that have alterations
106 
+	pct = rowSums(apply(arr, 1:2, any)) / ncol(mat_list[[1]])
107 
+	pct = paste0(round(pct * 100), "%")
108 
+	ha_pct = rowAnnotation(pct = row_anno_text(pct, just = "right", offset = unit(1, "npc"), gp = pct_gp), width = grobWidth(textGrob("100%", gp = pct_gp)))
109 
+
110 
+	#####################################################################
111 
+	# row annotation which is a barplot
112 
+	anno_row_bar = function(index, k = NULL, N = NULL) {
113 
+		n = length(index)
114 
+		count = apply(arr, c(1, 3), sum)[index, , drop = FALSE]
115 
+		max_count = max(rowSums(count))
116 
+		pushViewport(viewport(xscale = c(0, max_count*1.1), yscale = c(0.5, n + 0.5)))
117 
+		for(i in seq_len(nrow(count))) {
118 
+			if(any(count[i, ] > 0)) {
119 
+				x = count[i, ]
120 
+				x = x[x > 0]
121 
+				x2 = cumsum(x)
122 
+				type = all_type[count[i, ] > 0]
123 
+				# row order is from top to end while coordinate of y is from bottom to top
124 
+				# so here we need to use n-i+1
125 
+				grid.rect(x2, n-i+1, width = x, height = 0.8, default.units = "native", just = "right", gp = gpar(col = NA, fill = col[type]))
126 
+			}
127 
+		}
128 
+		breaks = grid.pretty(c(0, max_count))
129 
+		if(k == 1) {
130 
+			grid.xaxis(at = breaks, label = breaks, main = FALSE, gp = axis_gp)
131 
+		}
132 
+		upViewport()
133 
+	}
134 
+
135 
+	ha_row_bar = rowAnnotation(row_bar = anno_row_bar, width = row_barplot_width)
136 
+
137 
+	###################################################################
138 
+	# column annotation which is also a barplot
139 
+	anno_column_bar = function(index) {
140 
+		n = length(index)
141 
+		count = apply(arr, c(2, 3), sum)[index, , drop = FALSE]
142 
+		max_count = max(rowSums(count))
143 
+		pushViewport(viewport(yscale = c(0, max_count*1.1), xscale = c(0.5, n + 0.5)))
144 
+		for(i in seq_len(nrow(count))) {
145 
+			if(any(count[i, ] > 0)) {
146 
+				y = count[i, ]
147 
+				y = y[y > 0]
148 
+				y2 = cumsum(y)
149 
+				type = all_type[count[i, ] > 0]
150 
+				grid.rect(i, y2, height = y, width = 0.8, default.units = "native", just = "top", gp = gpar(col = NA, fill = col[type]))
151 
+			}
152 
+		}
153 
+		breaks = grid.pretty(c(0, max_count))
154 
+		grid.yaxis(at = breaks, label = breaks, gp = axis_gp)
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+		upViewport()
156 
+	}
157 
+
158 
+	ha_column_bar = HeatmapAnnotation(column_bar = anno_column_bar, which = "column", height = column_barplot_height)
159 
+
160 
+	#####################################################################
161 
+	# the main matrix
162 
+	pheudo = c(all_type, rep(NA, nrow(arr)*ncol(arr) - length(all_type)))
163 
+	dim(pheudo) = dim(arr[, , 1])
164 
+	dimnames(pheudo) = dimnames(arr[, , 1])
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+	if(show_column_barplot) {
166 
+		ht = Heatmap(pheudo, col = col, rect_gp = gpar(type = "none"),
167 
+			cluster_rows = FALSE, cluster_columns = FALSE,
168 
+			cell_fun = function(j, i, x, y, width, height, fill) {
169 
+				z = arr[i, j, ]
170 
+				add_oncoprint("background", x, y, width, height)
171 
+				for(type in all_type[z]) {
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+					add_oncoprint(type, x, y, width, height)
173 
+				}
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+			}, show_column_names = show_column_names,
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+			top_annotation = ha_column_bar, ...)
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+	} else {
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+		ht = Heatmap(pheudo, rect_gp = gpar(type = "none"),
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+			cluster_rows = FALSE, cluster_columns = FALSE,
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+			cell_fun = function(j, i, x, y, width, height, fill) {
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+				z = arr[i, j, ]
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+				add_oncoprint("background", x, y, width, height)
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+				for(type in all_type[z]) {
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+					add_oncoprint(type, x, y, width, height)
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+				}
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+			}, show_column_names = show_column_names, ...)
186 
+	}
187 
+
188 
+	if(show_row_barplot) {
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+		ht_list = ha_pct + ht + ha_row_bar
190 
+	} else {
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+		ht_list = ha_pct + ht
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+	}
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+
194 
+	return(ht_list)
195 
+
196 
+}
0 197 
\ No newline at end of file
vignettes/sample_order.txt
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1 198 
similarity index 100%
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rename from vignettes/sample_order.txt
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rename to inst/extdata/sample_order.txt
vignettes/tcga_lung_adenocarcinoma_provisional_ras_raf_mek_jnk_signalling.txt
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4 201 
similarity index 100%
5 202 
rename from vignettes/tcga_lung_adenocarcinoma_provisional_ras_raf_mek_jnk_signalling.txt
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rename to inst/extdata/tcga_lung_adenocarcinoma_provisional_ras_raf_mek_jnk_signalling.txt
man/Heatmap.rd
History View file @ 451e6d7
... ... 
@@ -7,8 +7,8 @@ Constructor method for Heatmap class
7 7 
 Constructor method for Heatmap class
8 8 
 }
9 9 
 \usage{
10 
-Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),
11 
-    cell_fun = function(j, i, x, y, width, height, fill) NULL,
10 
+Heatmap(matrix, col, name, na_col = "grey", color_space = "LAB",
11 
+    rect_gp = gpar(col = NA), cell_fun = function(j, i, x, y, width, height, fill) NULL,
12 12 
     row_title = character(0), row_title_side = c("left", "right"),
13 13 
     row_title_gp = gpar(fontsize = 14),
14 14 
     row_title_rot = switch(row_title_side[1], "left" = 90, "right" = 270),
... ... 
@@ -45,6 +45,7 @@ Heatmap(matrix, col, name, na_col = "grey", rect_gp = gpar(col = NA),
45 45 
   \item{name}{name of the heatmap. The name is used as the title of the heatmap legend.}
46 46 
   \item{na_col}{color for \code{NA} values.}
47 47 
   \item{rect_gp}{graphic parameters for drawing rectangles (for heatmap body).}
48 
+  \item{color_space}{the color space in which colors are interpolated. Only used if \code{matrix} is numeric and \code{col} is a vector of colors. Pass to \code{\link[circlize]{colorRamp2}}.}
48 49 
   \item{cell_fun}{self-defined function to add graphics on each cell. Seven parameters will be passed into this function: \code{i}, \code{j}, \code{x}, \code{y}, \code{width}, \code{height}, \code{fill} which are row index,column index in \code{matrix}, coordinate of the middle points in the heatmap body viewport,the width and height of the cell and the filled color. }
49 50 
   \item{row_title}{title on row.}
50 51 
   \item{row_title_side}{will the title be put on the left or right of the heatmap?}
man/densityHeatmap.rd
History View file @ 451e6d7
... ... 
@@ -8,13 +8,14 @@ Use colors to represent density distribution
8 8 
 }
9 9 
 \usage{
10 10 
 densityHeatmap(data, col = rev(brewer.pal(11, "Spectral")),
11 
-    anno = NULL, ylab = deparse(substitute(data)),
11 
+    color_space = "RGB", anno = NULL, ylab = deparse(substitute(data)),
12 12 
     title = paste0("Density heatmap of ", deparse(substitute(data))))
13 13 
 }
14 14 
 \arguments{
15 15
16 16 
   \item{data}{a matrix or a list. If it is a matrix, density will be calculated by columns.}
17 17 
   \item{col}{a list of colors that density values are scaled to.}
18 
+  \item{color_space}{the color space in which colors are interpolated. Pass to \code{\link[circlize]{colorRamp2}}.}
18 19 
   \item{anno}{annotation for matrix columns or list. The value should be a vector or a data frame. It can also be a \code{\link{HeatmapAnnotation-class}} object.}
19 20 
   \item{ylab}{label on y-axis in the plot}
20 21 
   \item{title}{title of the plot}
man/oncoPrint.rd
History View file @ 451e6d7
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new file mode 100644
... ... 
@@ -0,0 +1,43 @@
1 
+\name{oncoPrint}
2 
+\alias{oncoPrint}
3 
+\title{
4 
+Make oncoPrint
5 
+}
6 
+\description{
7 
+Make oncoPrint
8 
+}
9 
+\usage{
10 
+oncoPrint(mat, get_type = function(x) x,
11 
+    alter_fun_list, col, show_column_names = FALSE,
12 
+    pct_gp = gpar(), axis_gp = gpar(fontsize = 8),
13 
+    show_row_barplot = TRUE, row_barplot_width = unit(2, "cm"),
14 
+    show_column_barplot = TRUE, column_barplot_height = unit(2, "cm"),
15 
+    ...)
16 
+}
17 
+\arguments{
18 
+
19 
+  \item{mat}{a character matrix which encodes mulitple alterations or a list of matrix for which every matrix contains binaryvalue representing the alteration is present or absent. When it is a list, the names represent alteration types.}
20 
+  \item{get_type}{If different alterations are encoded in the matrix, this self-defined functiondetermines how to extract them. Only work when \code{mat} is a matrix.}
21 
+  \item{alter_fun_list}{a list of functions which define how to add graphics for different alterations.The names of the list should cover all alteration types.}
22 
+  \item{col}{a vector of color for which names correspond to alteration types.}
23 
+  \item{show_column_names}{whether show column names}
24 
+  \item{pct_gp}{graphic paramters for percent row annotation}
25 
+  \item{axis_gp}{graphic paramters for axes}
26 
+  \item{show_row_barplot}{whether show barplot annotation on rows}
27 
+  \item{row_barplot_width}{width of barplot annotation on rows. It should be a \code{\link[grid]{unit}} object}
28 
+  \item{show_column_barplot}{whether show barplot annotation on columns}
29 
+  \item{column_barplot_height}{height of barplot annotatioin on columns. it should be a \code{\link[grid]{unit}} object.}
30 
+  \item{...}{pass to \code{\link{Heatmap}}}
31 
+
32 
+}
33 
+\details{
34 
+The function returns a normal heatmap list and you can add more heatmaps/row annotations to it.
35 
+
36 
+For more explanation, please go to the vignette.
37 
+}
38 
+\value{
39 
+a \code{\link{HeatmapList-class}} object.
40 
+}
41 
+\author{
42 
+Zuguang Gu <z.gu@dkfz.de>
43 
+}
vignettes/mutation.txt
History View file @ 451e6d7
0 44 
deleted file mode 100644
... ... 
@@ -1,173 +0,0 @@
1 
-Case ID	KEAP1	TMTC1	OR4C16	ZNF676	STK11	TP53	KRAS	EGFR	CDKN2A	MAGEC1	NAV3	CDH10	MROH2B	OR5W2	OR5D14	RIT1	LRRTM4	NRG3	U2AF1	TBX22	BAGE2	OR4C15	ZNF492	FERD3L	OR2T34	CCDC178	SERPINB4	ZNF804A	PABPC3	EPHA6	ELTD1	OR2L3	REG1B	CD5L	CNBD1	REG3A	GABRB3	OR2T4	TRIM58	OR4A5	NRAS	BRAF	OR2L8	HGF	OR8H2	ADAMTS2	ZNF268	OR5I1	KCNT2	THEMIS	GBA3	ASTN2
2 
-TCGA-05-4384-01	MUT;	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	MUT;
3 
-TCGA-05-4390-01	  	MUT;	  	  	  	  	MUT;	  	  	  	MUT;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	MUT;
4 
-TCGA-05-4425-01	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
5 
-TCGA-38-4631-01	MUT;	  	  	MUT;	  	  	  	  	HOMDEL;	MUT;	MUT;	AMP;	  	  	MUT;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	MUT;	MUT;
6 
-TCGA-38-4632-01	  	  	  	  	  	MUT;	  	  	  	MUT;	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	MUT;	  	  	  	  	MUT;
7 
-TCGA-38-6178-01	  	  	  	  	  	MUT;	  	MUT;AMP;	MUT;HOMDEL;
8 
-TCGA-44-6144-01	  	  	  	MUT;	MUT;	MUT;	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
9 
-TCGA-44-6145-01	  	  	  	  	  	MUT;	MUT;	  	  	  	  	MUT;	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	AMP;	  	AMP;	MUT;	  	  	  	  	  	MUT;
10 
-TCGA-44-6146-01	  	  	  	  	  	  	MUT;
11 
-TCGA-44-6147-01	  	  	  	  	  	MUT;	  	MUT;
12 
-TCGA-44-6148-01
13 
-TCGA-49-4488-01	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	MUT;
14 
-TCGA-50-5930-01	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
15 
-TCGA-50-5931-01	  	  	  	MUT;	  	MUT;	  	  	  	  	  	AMP;	AMP;	  	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
16 
-TCGA-50-5932-01	  	  	  	  	MUT;	  	MUT;	  	HOMDEL;	MUT;	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	AMP;	  	  	  	  	  	AMP;	AMP;	  	  	  	AMP;
17 
-TCGA-50-5933-01	  	  	  	  	  	MUT;	MUT;	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	MUT;AMP;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;
18 
-TCGA-50-5935-01	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	MUT;
19 
-TCGA-50-5941-01	  	MUT;	MUT;	  	  	MUT;	MUT;AMP;	  	  	MUT;	MUT;	  	  	  	MUT;	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;
20 
-TCGA-50-5942-01	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	MUT;
21 
-TCGA-50-5944-01	  	  	  	  	  	MUT;	  	MUT;	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;
22 
-TCGA-50-5946-01	  	  	  	  	  	MUT;	  	  	HOMDEL;
23 
-TCGA-50-6591-01	  	  	  	  	  	MUT;	  	MUT;AMP;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
24 
-TCGA-50-6592-01	  	  	MUT;	  	HOMDEL;	MUT;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	MUT;	MUT;
25 
-TCGA-50-6593-01	  	  	  	  	  	MUT;	  	  	  	MUT;	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;
26 
-TCGA-50-6594-01	  	  	MUT;HOMDEL;	  	  	MUT;	  	  	AMP;	MUT;	  	AMP;	AMP;	HOMDEL;	HOMDEL;	  	  	  	  	  	  	HOMDEL;	  	  	MUT;	  	  	MUT;	  	  	MUT;	  	  	  	MUT;	  	  	MUT;	  	MUT;HOMDEL;	  	MUT;	  	  	HOMDEL;	AMP;	  	HOMDEL;
27 
-TCGA-55-6543-01
28 
-TCGA-67-4679-01	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
29 
-TCGA-67-6215-01	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	AMP;	  	  	  	MUT;	  	  	AMP;	  	MUT;AMP;	  	  	  	AMP;	AMP;	MUT;	  	  	AMP;	  	  	  	  	  	AMP;
30 
-TCGA-67-6216-01
31 
-TCGA-67-6217-01	  	  	  	  	  	  	  	MUT;	  	MUT;	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	AMP;
32 
-TCGA-73-4658-01	  	  	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
33 
-TCGA-73-4676-01	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	AMP;
34 
-TCGA-75-5122-01	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
35 
-TCGA-75-5125-01	  	MUT;	  	  	  	MUT;	  	  	HOMDEL;	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	MUT;
36 
-TCGA-75-5126-01	  	MUT;	  	  	  	  	MUT;	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;
37 
-TCGA-75-6203-01	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	MUT;
38 
-TCGA-75-6205-01
39 
-TCGA-75-6206-01	MUT;	  	  	  	  	  	MUT;
40 
-TCGA-75-6207-01	  	  	  	MUT;	  	MUT;	  	MUT;	  	MUT;	  	AMP;
41 
-TCGA-75-6211-01	MUT;	  	  	  	  	MUT;	HOMDEL;	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	  	MUT;	  	  	HOMDEL;	  	MUT;	  	  	MUT;	MUT;	  	MUT;	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	MUT;
42 
-TCGA-75-6212-01	  	  	  	  	  	  	  	MUT;
43 
-TCGA-86-6562-01	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	AMP;	  	AMP;	  	  	  	AMP;	AMP;	  	AMP;	  	AMP;	  	  	  	  	  	AMP;
44 
-TCGA-05-4396-01	  	MUT;	MUT;	  	  	MUT;	  	MUT;	  	MUT;	MUT;	MUT;AMP;	MUT;AMP;	  	  	MUT;AMP;	  	MUT;	  	MUT;	  	MUT;	  	  	AMP;	MUT;	  	MUT;	  	MUT;	MUT;	MUT;AMP;	  	MUT;AMP;	  	MUT;	MUT;	MUT;AMP;	AMP;	  	AMP;	  	MUT;AMP;	MUT;	MUT;	  	  	MUT;	MUT;AMP;	MUT;	  	MUT;AMP;
45 
-TCGA-05-4405-01	  	  	  	  	  	MUT;	MUT;	  	  	  	  	MUT;
46 
-TCGA-05-4410-01	  	  	  	  	  	MUT;	  	MUT;	  	MUT;	  	MUT;	MUT;	  	  	  	MUT;	MUT;	  	  	  	  	MUT;	  	  	MUT;	  	  	MUT;	  	  	  	  	MUT;	  	MUT;	  	MUT;	  	  	  	MUT;	  	MUT;	MUT;	  	  	  	MUT;	MUT;
47 
-TCGA-05-4415-01	HOMDEL;	MUT;	  	  	MUT;	  	MUT;	AMP;	  	  	MUT;	MUT;	  	MUT;
48 
-TCGA-05-4417-01	  	  	  	MUT;	MUT;	  	MUT;	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;
49 
-TCGA-05-4424-01	  	  	  	MUT;	  	MUT;	  	  	  	  	  	MUT;AMP;	MUT;AMP;	  	  	  	  	MUT;	  	  	  	  	  	MUT;	MUT;	  	MUT;	MUT;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	MUT;	MUT;
50 
-TCGA-05-4427-01	  	MUT;	  	  	  	MUT;	MUT;	  	  	MUT;	  	MUT;	MUT;	  	  	AMP;	  	MUT;	  	  	  	  	  	  	MUT;	  	  	MUT;	MUT;	MUT;	MUT;	MUT;	MUT;	  	MUT;	  	  	  	  	  	  	  	MUT;	MUT;	MUT;	MUT;	  	  	MUT;	  	  	MUT;AMP;
51 
-TCGA-05-4433-01	  	AMP;	  	  	  	MUT;	MUT;AMP;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;
52 
-TCGA-44-6774-01	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	MUT;
53 
-TCGA-44-6775-01	  	  	  	  	  	MUT;HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
54 
-TCGA-44-6776-01	MUT;	  	  	  	MUT;	  	MUT;	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;
55 
-TCGA-44-6777-01	  	  	  	MUT;	  	MUT;	MUT;	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	MUT;
56 
-TCGA-44-6778-01	MUT;	  	  	  	  	MUT;	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;	  	  	  	  	  	  	  	  	MUT;
57 
-TCGA-44-6779-01	MUT;	  	  	  	MUT;	MUT;	  	  	HOMDEL;	  	  	  	  	  	  	MUT;
58 
-TCGA-49-4487-01	  	  	MUT;	  	MUT;	MUT;	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	MUT;AMP;	  	  	  	  	  	  	AMP;	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
59 
-TCGA-49-4490-01	  	  	  	  	  	MUT;	  	MUT;	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;
60 
-TCGA-49-4512-01	  	  	  	  	  	  	  	  	  	  	  	MUT;
61 
-TCGA-49-4514-01	MUT;	  	  	  	  	MUT;	  	  	  	  	MUT;	MUT;	  	  	  	MUT;	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;
62 
-TCGA-49-6742-01	MUT;	  	  	  	  	  	  	  	HOMDEL;	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	MUT;
63 
-TCGA-49-6743-01	MUT;	  	MUT;	  	  	  	  	  	  	  	MUT;	MUT;	MUT;	  	  	  	MUT;	  	MUT;	MUT;	  	MUT;	  	  	  	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	MUT;
64 
-TCGA-49-6744-01	  	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
65 
-TCGA-49-6745-01	  	AMP;	  	  	  	  	AMP;	  	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;
66 
-TCGA-49-6767-01	  	  	  	  	  	MUT;	  	  	HOMDEL;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	MUT;	  	  	MUT;	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	MUT;
67 
-TCGA-50-5044-01	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	  	HOMDEL;	MUT;
68 
-TCGA-50-5051-01	MUT;	  	  	  	  	  	MUT;	  	  	MUT;
69 
-TCGA-50-5072-01	  	  	  	  	MUT;	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	MUT;
70 
-TCGA-50-6590-01	  	  	  	  	  	MUT;	  	  	  	MUT;AMP;	  	MUT;	MUT;	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;AMP;	  	  	  	  	  	MUT;	AMP;	  	  	  	  	MUT;	AMP;	MUT;AMP;	  	  	  	AMP;
71 
-TCGA-50-6595-01	  	  	  	  	  	MUT;	  	MUT;	MUT;
72 
-TCGA-50-6597-01	  	  	  	AMP;	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	AMP;	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;
73 
-TCGA-55-6642-01	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
74 
-TCGA-55-6712-01	  	  	  	  	  	MUT;	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;
75 
-TCGA-71-6725-01	  	  	MUT;
76 
-TCGA-91-6828-01	  	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	HOMDEL;
77 
-TCGA-91-6829-01	  	MUT;	  	  	  	MUT;	  	  	  	  	  	AMP;	AMP;	  	  	AMP;	  	  	  	  	  	MUT;	  	AMP;	AMP;	  	  	  	  	AMP;	MUT;	MUT;AMP;	  	AMP;	  	MUT;	  	AMP;	AMP;	  	  	  	AMP;	MUT;	  	  	  	  	  	  	MUT;	MUT;
78 
-TCGA-91-6831-01	  	  	MUT;	  	  	MUT;	  	  	HOMDEL;	  	HOMDEL;	MUT;	MUT;AMP;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	MUT;
79 
-TCGA-91-6835-01	  	AMP;	  	  	  	  	AMP;	MUT;	  	  	  	MUT;	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;
80 
-TCGA-91-6836-01	  	AMP;	  	  	  	MUT;	MUT;AMP;	  	  	  	MUT;	  	  	MUT;	  	MUT;AMP;	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;	  	  	  	  	  	AMP;	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	MUT;
81 
-TCGA-35-3615-01	MUT;	  	  	  	MUT;	  	MUT;	  	  	  	  	MUT;	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	HOMDEL;	  	  	HOMDEL;
82 
-TCGA-44-2655-01	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	AMP;	  	AMP;	  	  	  	AMP;	MUT;AMP;	  	  	  	AMP;	  	  	  	  	  	AMP;
83 
-TCGA-44-2656-01	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	MUT;	MUT;	MUT;	  	MUT;	  	MUT;	  	  	  	  	  	  	  	  	  	  	MUT;
84 
-TCGA-44-2659-01	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	MUT;
85 
-TCGA-44-2662-01	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	MUT;
86 
-TCGA-44-2665-01	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	MUT;
87 
-TCGA-44-2666-01	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
88 
-TCGA-44-2668-01	  	  	  	  	  	MUT;	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	MUT;	MUT;	  	  	MUT;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
89 
-TCGA-55-1592-01	  	  	  	  	  	MUT;	AMP;	  	HOMDEL;	AMP;	  	AMP;	AMP;	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	AMP;	  	MUT;	  	  	  	  	AMP;	  	  	  	  	MUT;	  	  	MUT;
90 
-TCGA-55-1594-01	  	  	  	  	  	MUT;	  	AMP;	MUT;
91 
-TCGA-55-1595-01	  	  	MUT;	MUT;	  	  	MUT;	  	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	  	MUT;	MUT;
92 
-TCGA-55-1596-01	  	  	  	  	MUT;	MUT;	  	  	  	  	  	  	AMP;	  	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	MUT;
93 
-TCGA-64-1676-01	  	  	  	  	  	MUT;	  	  	  	  	  	  	MUT;	  	  	AMP;	MUT;AMP;	  	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	MUT;	MUT;	  	MUT;	  	  	MUT;	  	  	AMP;
94 
-TCGA-64-1677-01	  	  	  	  	  	MUT;	MUT;	  	  	MUT;	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	HOMDEL;	MUT;	  	MUT;
95 
-TCGA-64-1678-01	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	MUT;
96 
-TCGA-64-1680-01	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	  	MUT;
97 
-TCGA-67-3770-01	  	  	  	  	  	MUT;	  	MUT;	HOMDEL;	  	  	MUT;
98 
-TCGA-67-3771-01	MUT;	MUT;	  	MUT;	  	MUT;	  	  	MUT;	  	MUT;	MUT;	  	  	  	AMP;	  	  	  	  	AMP;	  	  	  	MUT;	  	  	MUT;AMP;	MUT;	MUT;AMP;	  	  	  	AMP;
99 
-TCGA-67-3772-01	  	  	  	  	  	  	  	MUT;	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
100 
-TCGA-67-3773-01	  	  	  	  	  	  	MUT;	  	  	AMP;	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
101 
-TCGA-67-3774-01	MUT;	  	  	  	MUT;	  	MUT;AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
102 
-TCGA-05-4244-01	  	  	  	MUT;	AMP;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	MUT;	  	  	HOMDEL;	  	  	  	  	  	HOMDEL;	HOMDEL;	  	  	  	HOMDEL;	  	  	  	MUT;	  	MUT;
103 
-TCGA-05-4249-01	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	AMP;	MUT;	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	AMP;	  	AMP;	  	  	  	AMP;	AMP;	  	  	MUT;	AMP;	  	  	  	  	  	AMP;	  	  	MUT;
104 
-TCGA-05-4250-01	  	MUT;AMP;	  	  	  	  	MUT;AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	MUT;	MUT;
105 
-TCGA-35-4122-01	  	  	  	  	  	MUT;	  	  	HOMDEL;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	AMP;	  	  	MUT;
106 
-TCGA-35-4123-01	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;	  	  	  	  	  	  	MUT;
107 
-TCGA-44-2657-01	  	AMP;	  	  	  	  	AMP;	  	  	  	  	MUT;AMP;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	MUT;
108 
-TCGA-44-2661-01
109 
-TCGA-44-3398-01	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;
110 
-TCGA-44-3918-01	  	MUT;AMP;	  	  	  	MUT;	  	  	  	  	MUT;	MUT;	MUT;	  	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	MUT;	  	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	MUT;	MUT;	MUT;	  	  	MUT;
111 
-TCGA-44-3919-01
112 
-TCGA-44-4112-01	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;	  	  	AMP;	MUT;
113 
-TCGA-05-4382-01	HOMDEL;	  	MUT;	MUT;	HOMDEL;	MUT;	  	MUT;	HOMDEL;	MUT;	MUT;	MUT;	MUT;	MUT;	MUT;	  	MUT;	  	  	MUT;	  	  	  	  	AMP;	MUT;	  	MUT;	  	MUT;	  	MUT;AMP;	  	MUT;	  	  	MUT;	MUT;AMP;	AMP;	  	  	MUT;	MUT;AMP;	MUT;	  	MUT;	  	  	MUT;
114 
-TCGA-05-4389-01	MUT;	  	  	  	  	  	  	  	HOMDEL;	MUT;	MUT;	MUT;	  	  	  	AMP;	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
115 
-TCGA-05-4395-01	MUT;	  	  	  	MUT;	MUT;	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	MUT;
116 
-TCGA-05-4397-01	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	MUT;	  	  	  	AMP;	  	  	MUT;	  	  	  	AMP;	  	MUT;AMP;	MUT;	MUT;	  	AMP;	AMP;	  	  	  	AMP;	  	  	MUT;	MUT;	  	AMP;	  	  	MUT;
117 
-TCGA-05-4398-01	  	MUT;	  	  	  	MUT;HOMDEL;	  	  	  	  	MUT;	MUT;	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
118 
-TCGA-05-4402-01	  	  	  	  	  	MUT;	  	MUT;AMP;	HOMDEL;
119 
-TCGA-05-4403-01	  	  	  	  	  	  	MUT;	  	HOMDEL;	  	  	  	MUT;
120 
-TCGA-05-4418-01	MUT;	  	  	MUT;	  	  	MUT;	  	HOMDEL;	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;
121 
-TCGA-05-4420-01	  	MUT;	  	  	  	MUT;	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
122 
-TCGA-05-4422-01	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	MUT;
123 
-TCGA-05-4426-01	  	  	  	  	  	MUT;	  	  	MUT;	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;
124 
-TCGA-05-4430-01	  	MUT;	  	  	  	MUT;	MUT;	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	MUT;	MUT;
125 
-TCGA-05-4432-01	  	  	  	  	MUT;	MUT;	  	  	HOMDEL;	MUT;	MUT;	  	  	  	MUT;	  	MUT;	MUT;	  	  	HOMDEL;	  	  	  	  	  	  	MUT;	  	  	  	MUT;	  	AMP;	  	MUT;	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	MUT;
126 
-TCGA-05-4434-01	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	AMP;	  	  	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	AMP;
127 
-TCGA-38-4625-01	  	MUT;	  	  	  	MUT;	  	  	MUT;HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
128 
-TCGA-38-4626-01	  	  	  	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	MUT;	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
129 
-TCGA-38-4627-01	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	MUT;
130 
-TCGA-38-4628-01	  	  	  	  	  	  	  	MUT;AMP;	HOMDEL;	  	  	  	AMP;	  	  	AMP;	  	  	  	MUT;	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;
131 
-TCGA-38-4629-01	  	  	  	  	  	MUT;	  	MUT;	HOMDEL;	  	  	  	MUT;AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;
132 
-TCGA-38-4630-01	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	AMP;
133 
-TCGA-44-3396-01	  	  	  	  	  	MUT;HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;
134 
-TCGA-49-4486-01	MUT;	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;
135 
-TCGA-49-4494-01	  	  	  	  	  	  	  	MUT;	HOMDEL;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	MUT;	  	  	  	  	  	HOMDEL;
136 
-TCGA-49-4501-01	  	  	  	  	  	  	  	MUT;AMP;	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
137 
-TCGA-49-4505-01	  	  	  	  	  	MUT;	MUT;	  	MUT;	  	MUT;	AMP;	MUT;	  	  	  	  	  	MUT;
138 
-TCGA-49-4506-01	MUT;	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	AMP;	  	  	  	  	  	  	  	  	AMP;	  	  	MUT;	  	  	  	AMP;	  	AMP;	  	  	  	AMP;	AMP;	  	  	  	AMP;	MUT;	  	  	  	  	AMP;
139 
-TCGA-49-4507-01	MUT;	AMP;	  	  	MUT;	  	AMP;	  	HOMDEL;	  	  	  	  	MUT;	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
140 
-TCGA-49-4510-01	  	AMP;	  	  	  	  	MUT;AMP;	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	AMP;
141 
-TCGA-73-4659-01	  	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	MUT;	  	AMP;	  	  	  	  	  	AMP;	AMP;	  	  	  	AMP;	  	  	MUT;
142 
-TCGA-73-4662-01	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	AMP;	AMP;	MUT;	  	MUT;	  	MUT;	  	AMP;	  	AMP;	  	  	  	AMP;	AMP;	  	  	  	AMP;	  	  	  	  	  	AMP;	  	AMP;
143 
-TCGA-73-4666-01	MUT;	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	AMP;
144 
-TCGA-73-4668-01	  	MUT;	  	MUT;	  	  	AMP;	  	HOMDEL;	  	MUT;	AMP;	AMP;	  	MUT;	  	  	MUT;	  	  	  	MUT;	  	  	  	  	MUT;	MUT;	  	  	MUT;	  	MUT;
145 
-TCGA-73-4670-01	MUT;	MUT;	  	  	MUT;	MUT;	MUT;	  	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;
146 
-TCGA-73-4675-01	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
147 
-TCGA-73-4677-01	MUT;	  	  	  	MUT;	  	MUT;	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
148 
-TCGA-05-5420-01
149 
-TCGA-05-5423-01	  	  	  	  	  	MUT;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	AMP;	  	  	  	  	  	MUT;AMP;	AMP;	  	  	  	AMP;
150 
-TCGA-05-5425-01	  	AMP;
151 
-TCGA-05-5428-01	  	  	  	  	  	MUT;	  	  	  	  	  	AMP;	AMP;	  	  	  	  	  	  	  	  	MUT;	  	  	  	MUT;	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;AMP;	  	MUT;	MUT;	  	  	MUT;
152 
-TCGA-05-5429-01	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
153 
-TCGA-05-5715-01	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;
154 
-TCGA-35-5375-01	MUT;	  	  	  	  	MUT;	  	  	  	  	  	AMP;	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	  	  	MUT;	MUT;	  	  	  	  	MUT;	  	MUT;
155 
-TCGA-44-5643-01	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	MUT;
156 
-TCGA-44-5645-01	  	  	  	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;AMP;
157 
-TCGA-50-5045-01	  	MUT;	  	  	  	MUT;	  	  	  	  	MUT;	MUT;AMP;	AMP;	  	MUT;	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	MUT;
158 
-TCGA-50-5049-01	  	  	MUT;	  	  	MUT;	  	  	  	  	MUT;	MUT;	  	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	  	MUT;	MUT;	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	MUT;
159 
-TCGA-50-5055-01
160 
-TCGA-50-5066-01	  	  	MUT;	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;
161 
-TCGA-50-5068-01	MUT;	  	  	  	  	MUT;	  	  	HOMDEL;	  	MUT;	MUT;
162 
-TCGA-50-5936-01	MUT;	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;
163 
-TCGA-50-5939-01	MUT;	  	  	  	MUT;	MUT;	  	AMP;	  	  	MUT;
164 
-TCGA-55-5899-01	MUT;	  	  	MUT;HOMDEL;	  	MUT;	  	  	HOMDEL;	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	  	  	MUT;	  	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	  	HOMDEL;
165 
-TCGA-64-5774-01	  	  	HOMDEL;	  	  	  	MUT;	  	  	  	  	MUT;	  	HOMDEL;	HOMDEL;	  	MUT;	  	  	  	  	HOMDEL;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	HOMDEL;	  	  	HOMDEL;
166 
-TCGA-64-5775-01	  	  	  	  	  	MUT;	MUT;	  	  	  	  	  	  	  	  	  	HOMDEL;	  	  	MUT;	  	  	  	  	  	MUT;	  	  	  	  	AMP;
167 
-TCGA-64-5778-01	  	  	  	  	  	MUT;	MUT;	  	  	MUT;	  	MUT;AMP;	AMP;	  	MUT;	  	  	  	  	MUT;	  	  	  	  	  	MUT;	  	MUT;	  	MUT;	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;	MUT;
168 
-TCGA-64-5779-01	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	MUT;	MUT;	  	  	  	  	  	  	  	  	HOMDEL;	  	  	  	  	  	MUT;
169 
-TCGA-64-5781-01	MUT;	MUT;	MUT;	MUT;	  	  	  	  	  	  	MUT;	MUT;	MUT;	  	  	  	MUT;	  	  	MUT;	MUT;	  	  	MUT;	  	  	  	MUT;	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	MUT;	  	  	MUT;	  	  	  	MUT;
170 
-TCGA-64-5815-01	  	  	  	  	  	  	MUT;	  	HOMDEL;	MUT;AMP;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	AMP;
171 
-TCGA-75-5146-01	  	  	  	  	MUT;	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	  	  	  	MUT;	  	  	  	MUT;
172 
-TCGA-75-5147-01	  	  	  	  	  	MUT;	  	  	  	  	  	AMP;	AMP;
173 
-TCGA-80-5611-01	  	  	  	  	  	  	  	  	  	  	  	  	  	  	MUT;	AMP;	MUT;	  	  	  	MUT;	  	  	  	  	  	  	  	  	  	  	  	  	AMP;
vignettes/oncoprint.R
History View file @ 451e6d7
174 0 
deleted file mode 100644
... ... 
@@ -1,123 +0,0 @@
1 
-library(ComplexHeatmap)
2 
-library(GetoptLong)
3 
-
4 
-mat = read.table("tcga_lung_adenocarcinoma_provisional_ras_raf_mek_jnk_signalling.txt", header = TRUE,stringsAsFactors=FALSE, sep = "\t")
5 
-mat[is.na(mat)] = ""
6 
-rownames(mat) = mat[, 1]
7 
-mat = mat[, -1]
8 
-mat=  mat[, -ncol(mat)]
9 
-mat = t(as.matrix(mat))
10 
-
11 
-sample_order = scan("sample_order.txt", what = "character")
12 
-mat = mat[, sample_order]
13 
-
14 
-mat_origin = mat
15 
-mat = mat[, !apply(mat, 2, function(x) all(grepl("^\\s*$", x)))]
16 
-
17 
-altered = ncol(mat)/ncol(mat_origin)
18 
-
19 
-type_col = c("AMP" = "red", "HOMDEL"= "blue", "MUT" = "#008000")
20 
-type_name = c("AMP" = "Amplification", "HOMDEL" = "Deep deletion", "MUT" = "Mutation")
21 
-
22 
-
23 
-add_oncoprint = function(type, x, y, width, height) {
24 
-	if(any(type %in% "")) {
25 
-		grid.rect(x, y, width - unit(0.5, "mm"), height - unit(1, "mm"), gp = gpar(col = NA, fill = "#CCCCCC"))
26 
-	}
27 
-	if(any(type %in% "AMP")) {
28 
-		grid.rect(x, y, width - unit(0.5, "mm"), height - unit(1, "mm"), gp = gpar(col = NA, fill = type_col["AMP"]))
29 
-	}
30 
-	if(any(type %in% "HOMDEL")) {
31 
-		grid.rect(x, y, width - unit(0.5, "mm"), height - unit(1, "mm"), gp = gpar(col = NA, fill = type_col["HOMDEL"]))
32 
-	}
33 
-	if(any(type %in% "MUT")) {
34 
-		grid.rect(x, y, width - unit(0.5, "mm"), height*(1/3), gp = gpar(col = NA, fill = type_col["MUT"]))
35 
-	}
36 
-}
37 
-
38 
-#####################################################################
39 
-# row annotation which shows percent of mutations in all samples
40 
-pct = apply(mat_origin, 1, function(x) sum(!grepl("^\\s*$", x))/length(x))*100
41 
-pct = paste0(round(pct),"%")
42 
-ha_pct = rowAnnotation(pct = anno_text(pct, which = "row"), width = grobWidth(textGrob("100%", gp = gpar(fontsize = 10))))
43 
-
44 
-
45 
-#####################################################################
46 
-# row annotation which is a barplot
47 
-anno_row_bar = function(index) {
48 
-	n = length(index)
49 
-	tb = apply(mat[index, ], 1, function(x) {
50 
-		x = unlist(strsplit(x, ";"))
51 
-		x = x[!grepl("^\\s*$", x)]
52 
-		x = sort(x)
53 
-		table(x)
54 
-	})
55 
-	max_count = max(sapply(tb, sum))
56 
-	pushViewport(viewport(xscale = c(0, max_count*1.1), yscale = c(0.5, n + 0.5)))
57 
-	for(i in seq_along(tb)) {
58 
-		if(length(tb[[i]])) {
59 
-			x = cumsum(tb[[i]])
60 
-			# row order is from top to end while coordinate of y is from bottom to top
61 
-			# so here we need to use n-i+1
62 
-			grid.rect(x, n-i+1, width = tb[[i]], height = 0.8, default.units = "native", just = "right", gp = gpar(col = NA, fill = type_col[names(tb[[i]])]))
63 
-		}
64 
-	}
65 
-	breaks = grid.pretty(c(0, max_count))
66 
-	grid.xaxis(at = breaks, label = breaks, main = FALSE, gp = gpar(fontsize = 10))
67 
-	upViewport()
68 
-}
69 
-
70 
-ha_row_bar = rowAnnotation(row_bar = anno_row_bar, width = unit(4, "cm"))
71 
-
72 
-###################################################################
73 
-# column annotation which is also a barplot
74 
-anno_column_bar = function(index) {
75 
-	n = length(index)
76 
-	tb = apply(mat[, index], 2, function(x) {
77 
-		x = unlist(strsplit(x, ";"))
78 
-		x = x[!grepl("^\\s*$", x)]
79 
-		x = sort(x)
80 
-		table(x)
81 
-	})
82 
-	max_count = max(sapply(tb, sum))
83 
-	pushViewport(viewport(yscale = c(0, max_count*1.1), xscale = c(0.5, n + 0.5)))
84 
-	for(i in seq_along(tb)) {
85 
-		if(length(tb[[i]])) {
86 
-			y = cumsum(tb[[i]])
87 
-			grid.rect(i, y, height = tb[[i]], width = 0.8, default.units = "native", just = "top", gp = gpar(col = NA, fill = type_col[names(tb[[i]])]))
88 
-		}
89 
-	}
90 
-	breaks = grid.pretty(c(0, max_count))
91 
-	grid.yaxis(at = breaks, label = breaks, gp = gpar(fontsize = 10))
92 
-	upViewport()
93 
-}
94 
-
95 
-ha_column_bar = HeatmapAnnotation(column_bar = anno_column_bar, which = "column")
96 
-
97 
-
98 
-
99 
-#####################################################################
100 
-# the main matrix
101 
-ht = Heatmap(mat, rect_gp = gpar(type = "none"), cell_fun = function(j, i, x, y, width, height, fill) {
102 
-	if(grepl("^\\s*$", mat[i, j])) {
103 
-		type = ""
104 
-	} else {
105 
-		type = unique(strsplit(mat[i, j], ";")[[1]])
106 
-	}
107 
-	if(setequal(type, "MUT")) {
108 
-		type = c("MUT", "")
109 
-	}
110 
-	add_oncoprint(type, x, y, width, height)
111 
-}, row_names_gp = gpar(fontsize = 10), show_column_names = FALSE, show_heatmap_legend = FALSE,
112 
-top_annotation = ha_column_bar, top_annotation_height = unit(2, "cm"))
113 
-
114 
-ht_list = ha_pct + ht + ha_row_bar
115 
-
116 
-#########################################################
117 
-# legend
118 
-legend = legendGrob(labels = type_name[names(type_col)], pch = 15, gp = gpar(col = type_col), nrow = 1)
119 
-
120 
-#pdf("oncoprint.pdf", width = 10, height = 10)
121 
-draw(ht_list, newpage = FALSE, annotation_legend_side = "bottom", annotation_legend_list = list(legend), column_title = qq("OncoPrint for TCGA Lung Adenocarcinoma, genes in Ras Raf MEK JNK signalling.\nAltered in @{ncol(mat)}/@{ncol(mat_origin)} (@{round(altered*100)}% of cases)"), column_title_gp = gpar(fontsize = 12, fontface = "bold"))
122 
-#dev.off()
123 
-
vignettes/s1.introduction.Rmd
History View file @ 451e6d7
... ... 
@@ -68,7 +68,7 @@ to get full use of the package.
68 68 
 There are several vignettes in the package. Each vignette focuses on a specific topic. Following
69 69 
 lists the general topics discussed in these vignettes:
70 70
71 
-  1. [**Making a single Heatmap**](1.single_heatmap.html)
71 
+  1. [**Making a single Heatmap**](s2.single_heatmap.html)
72 72
73 73 
     This vignette introduces the basic configuration for making a single heatmap. Similar as other
74 74 
     R functions/packages, the basic usage is quite similar, but there are several unique features
... ... 
@@ -90,28 +90,32 @@ lists the general topics discussed in these vignettes:
90 90 
       different levels that split the heatmap.
91 91 
     - The heatmap body itself can be completely self-defined.
92 92
93 
-  2. [**Making a list of heatmaps**](2.a_list_of_heatmaps.html)
93 
+  2. [**Making a list of heatmaps**](s3.a_list_of_heatmaps.html)
94 94
95 95 
     This vignette introduces how to concatenate a list of heatmaps and how adjustment is applied to keep
96 96 
     the correspondence of the heatmaps.
97 97
98 
-  3. [**Heatmap annotations**](3.heatmap_annotation.html)
98 
+  3. [**Heatmap annotations**](s4.heatmap_annotation.html)
99 99
100 100 
     This vignette introduces the concept of the heatmap annotation and demonstrate how to make simple annotations
101 101 
     as well as complex annotations. Also, the vignette explains the difference between column annotations
102 102 
     and row annotations.
103 103
104 
-  4. [**Heatmap and Annotation Legends**](4.legend.html)
104 
+  4. [**Heatmap and Annotation Legends**](s5.legend.html)
105 105
106 106 
     This vignette introduces how to configurate the heatmap legend and annotation legend, also
107 107 
     how to add self-defined legends.
108 108
109 
-  5. [**Heatmap decoration**](5.heatmap_decoration.html)
109 
+  5. [**Heatmap decoration**](s6.heatmap_decoration.html)
110 110
111 111 
     This vignette introduces methods to add more self-defined graphics to the heatmaps after the heatmaps
112 112 
     are generated.
113 113
114 
-  6. [**Examples**](6.examples.html)
114 
+  6. [**Examples**](s7.examples.html)
115 115
116 116 
     More simulated and real-world examples are shown in this vignette.
117 
+
118 
+  7. [**OncoPrint**](s8.oncoprint.html)
117 119
120 
+    How to make an oncoPrint.
121 
+
vignettes/s2.single_heatmap.Rmd
History View file @ 451e6d7
... ... 
@@ -117,8 +117,8 @@ mat_with_na[sample(c(TRUE, FALSE), nrow(mat)*ncol(mat), replace = TRUE, prob = c
117 117 
 Heatmap(mat_with_na, na_col = "orange")
118 118 
 ```
119 119
120 
-Color space is important for interpolating colors. By default, colors are linearly interpolated in [LAB](https://en.wikipedia.org/wiki/Lab_color_space), but you can select the color space in `colorRamp2()` function. Compare following two plots
121 
-(`+` operation on two heatmaps will be introduced in [**Making a list of heatmaps**](a3.a_list_of_heatmap.html) vignette):
120 
+Color space is important for interpolating colors. By default, colors are linearly interpolated in [LAB color space](https://en.wikipedia.org/wiki/Lab_color_space), but you can select the color space in `colorRamp2()` function. Compare following two plots
121 
+(`+` operation on two heatmaps will be introduced in [**Making a list of heatmaps**](s3.a_list_of_heatmaps.html) vignette):
122 122
123 123 
 ```{r, fig.width = 10}
124 124 
 f1 = colorRamp2(seq(min(mat), max(mat), length = 3), c("blue", "#EEEEEE", "red"))
... ... 
@@ -127,22 +127,39 @@ Heatmap(mat, col = f1, column_title = "LAB color space") +
127 127 
 Heatmap(mat, col = f2, column_title = "RGB color space")
128 128 
 ```
129 129
130 
-On following figure, corresponding values change evenly on x-axis, you can see how colors change under different
131 
-color spaces. Choosing a proper color space is a little bit subjective and it depends on specific data and color theme.
130 
+On following figure, corresponding values change evenly on the folded axis, you can see how colors change under different
131 
+color spaces (the plot is made by **HilbertCurve** package). Choosing a proper color space is a little bit
132 
+subjective and it depends on specific data and color theme.
132 133 
 Sometimes you need to try several color spaces to determine one which can best reveal potential structure of your data.
133 134
134 
-```{r, fig.width = 10, fig.height = 4}
135 
-space = c("RGB", "LAB", "XYZ", "sRGB", "LUV")
136 
-x = seq(-1, 1, length = 100)
137 135
138 
-par(xpd = NA)
139 
-plot(NULL, xlim = c(-1, 1), ylim = c(0.5, length(space)-0.5), type = "n", axes = FALSE, ann = FALSE)
136 
+```{r, fig.width = 14, fig.height = 14/5, echo = FALSE, message = FALSE}
137 
+suppressPackageStartupMessages(library(HilbertCurve))
138 
+space = c("RGB", "LAB", "XYZ", "sRGB", "LUV")
139 
+pushViewport(viewport(layout = grid.layout(nr = 1, nc = length(space))))
140 140 
 for(i in seq_along(space)) {
141 
-    f = colorRamp2(c(-1, 0, 1), c("blue", "#EEEEEE", "red"), space = space[i])
142 
-    rect(x - 1/100, i - 0.5, x + 1/100, i + 0.5, col = f(x), border = NA)
143 
-    text(1, i, space[i], adj = c(-0.2, 0.5))
141 
+    pushViewport(viewport(layout.pos.row = 1, layout.pos.col = i))
142 
+    hc = HilbertCurve(1, 100, level = 4, newpage = FALSE, title = space[i])
143 
+    ir = IRanges(start = 1:99, end = 2:100)
144 
+    f = colorRamp2(c(-1, 0, 1), c("green", "black", "red"), space = space[i])
145 
+    col = f(seq(-1, 1, length = 100))
146 
+    hc_points(hc, ir, np = 3, gp = gpar(col = col, fill = col))
147 
+    upViewport()
144 148 
 }
145 
-axis(side = 1)
149 
+upViewport()
150 
+grid.newpage()
151 
+pushViewport(viewport(layout = grid.layout(nr = 1, nc = length(space))))
152 
+for(i in seq_along(space)) {
153 
+    pushViewport(viewport(layout.pos.row = 1, layout.pos.col = i))
154 
+    hc = HilbertCurve(1, 100, level = 4, newpage = FALSE, title = space[i])
155 
+    ir = IRanges(start = 1:99, end = 2:100)
156 
+    f = colorRamp2(c(-1, 0, 1), c("blue", "white", "red"), space = space[i])
157 
+    col = f(seq(-1, 1, length = 100))
158 
+    hc_points(hc, ir, np = 3, gp = gpar(col = col, fill = col))
159 
+    upViewport()
160 
+}
161 
+upViewport()
162 
+
146 163 
 ```
147 164
148 165 
 ## Titles
... ... 
@@ -150,14 +167,14 @@ axis(side = 1)
150 167 
 The name of the heatmap by default is used as the title of the heatmap legend.
151 168 
 The name also plays as a unique id if you plot more than one heatmaps together.
152 169 
 Later we can use this name to go to the corresponding heatmap to add more graphics
153 
-(see [**Heatmap Decoration**](5.heatmap_decoration.html) vignette).
170 
+(see [**Heatmap Decoration**](s6.heatmap_decoration.html) vignette).
154 171
155 172 
 ```{r with_matrix_name}
156 173 
 Heatmap(mat, name = "foo")
157 174 
 ```
158 175
159 176 
 The title of the heatmap legend can be modified by `heatmap_legend_param`
160 
-(see [**Heatmap and Annotation Legends**](4.legend.html) vignette
177 
+(see [**Heatmap and Annotation Legends**](s5.legend.html) vignette
161 178 
 for more control on the legend).
162 179
163 180 
 ```{r heatmap_legend_title}
... ... 
@@ -348,10 +365,10 @@ Heatmap(mat, name = "foo", row_names_gp = gpar(col = c(rep("red", 4), rep("blue"
348 365
349 366 
 Currently, rotations for column names and row names are not supported (or maybe in the future versions). Because
350 367 
 after the text rotation, the dimension names will go inside other heatmap components
351 
-which will mess up the heatmap layout. However, as will be introduced in [**Heatmap Annotation**](3.heatmap_annotation.html)
368 
+which will mess up the heatmap layout. However, as will be introduced in [**Heatmap Annotation**](s4.heatmap_annotation.html)
352 369 
 vignette, text rotation is allowed in the heatmap annotations. Thus, users can provide a row annotation
353 370 
 or column annotation which only contains rotated text to simulate rotated row/column names (You will see the
354 
-example in the [**Heatmap Annotation**](3.heatmap_annotation.html) vignette).
371 
+example in the [**Heatmap Annotation**](s4.heatmap_annotation.html) vignette).
355 372
356 373 
 ## Split heatmap by rows
357 374
vignettes/s3.a_list_of_heatmaps.Rmd
History View file @ 451e6d7
... ... 
@@ -31,7 +31,7 @@ options(width = 100)
31 31
32 32 
 A list of heatmaps can improve visualization of the correspondence between multiple data sources.
33 33 
 In this vignette, we will discuss configurations for making a list of heatmaps and you can
34 
-see more real-world examples in the [**Examples**](6.examples.html) vignette.
34 
+see more real-world examples in the [**Examples**](s7.examples.html) vignette.
35 35
36 36 
 ## Heatmap concatenation
37 37
... ... 
@@ -167,7 +167,7 @@ ht_global_opt(RESET = TRUE)
167 167 
 ## Heatmap list with row annotations
168 168
169 169 
 Row annotations can also be reordered and split according to the main heatmap,
170 
-please see [**Heatmap Annotation**](3.heatmap_annotationhtml) for more explanations.
170 
+please see [**Heatmap Annotation**](s4.heatmap_annotation.html) for more explanations.
171 171
172 172 
 ## Session info
173 173
vignettes/s7.examples.Rmd
History View file @ 451e6d7
... ... 
@@ -53,18 +53,6 @@ Heatmap(expr$chr, name = "chr", col = rand_color(length(unique(expr$chr))),
53 53 
     width = unit(5, "mm"))
54 54 
 ```
55 55
56 
-### Show number of alterations for OncoPrint
57 
-
58 
-Following examples is <a href="http://www.cbioportal.org/faq.jsp#what-are-oncoprints">OncoPrint</a>.
59 
-The basic idea is to self define the heatmap body. Besides the default style which is
60 
-provided by <a href="http://www.cbioportal.org/index.do">cBioPortal</a>, there are
61 
-additional barplots at both sides of the heatmap which show numbers of different alterations for
62 
-each sample and for each gene. Source code is available <a href="https://github.com/jokergoo/ComplexHeatmap/blob/master/vignettes/oncoprint.R">here</a>.
63 
-
64 
-```{r, echo = FALSE, fig.width = 10, fig.height = 8}
65 
-source("oncoprint.R")
66 
-```
67 
-
68 56 
 ### Visualize genomic regions and other correspondance
69 57
70 58 
 Following examples visualizes correlation between methylation and expression, as well as other annotation information (data are randomly generated). In the heatmap, each row corresponds to a differentially methylated regions (DMRs).
vignettes/s8.oncoprint.Rmd
History View file @ 451e6d7
71 59 
new file mode 100644
... ... 
@@ -0,0 +1,189 @@
1 
+
2 
+<!--
3 
+%\VignetteEngine{knitr}
4 
+%\VignetteIndexEntry{OncoPrint}
5 
+-->
6 
+
7 
+OncoPrint
8 
+========================================
9 
+
10 
+**Author**: Zuguang Gu ( z.gu@dkfz.de )
11 
+
12 
+**Date**: `r Sys.Date()`
13 
+
14 
+-------------------------------------------------------------
15 
+
16 
+```{r global_settings, echo = FALSE, message = FALSE}
17 
+library(markdown)
18 
+options(markdown.HTML.options = c(options('markdown.HTML.options')[[1]], "toc"))
19 
+
20 
+library(knitr)
21 
+knitr::opts_chunk$set(
22 
+    error = FALSE,
23 
+    tidy  = FALSE,
24 
+    message = FALSE,
25 
+    fig.align = "center",
26 
+    fig.width = 5,
27 
+    fig.height = 5)
28 
+options(markdown.HTML.stylesheet = "custom.css")
29 
+
30 
+options(width = 100)
31 
+```
32 
+
33 
+<a href="http://www.cbioportal.org/faq.jsp#what-are-oncoprints">OncoPrint</a> is a way to visualize
34 
+multiple genomic alteration events by heatmap. Here the **ComplexHeatmap** package provides a `oncoPrint()` function.
35 
+Besides the default style which is provided by <a href="http://www.cbioportal.org/index.do">cBioPortal</a>, there are
36 
+additional barplots at both sides of the heatmap which show numbers of different alterations for
37 
+each sample and for each gene. Also with the functionality of **ComplexHeatmap**, you can control oncoPrint with
38 
+more flexibilities.
39 
+
40 
+There are two different forms of input data. The first is represented as a matrix in which
41 
+element would include multiple alterations in a form of a complex string. In follow example,
42 
+'g1' in 's1' has two types of alterations which are 'snv' and 'indel'.
43 
+
44 
+```{r}
45 
+mat = read.table(textConnection(
46 
+"	s1	s2	s3
47 
+g1	snv;indel	snv	indel
48 
+g2		snv;indel	snv
49 
+g3	snv		indel;snv"), row.names = 1, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
50 
+mat = as.matrix(mat)
51 
+mat
52 
+```
53 
+
54 
+In this case, we need to define a function to extract different alteration types and send the function
55 
+to `get_type` argument. The function should return a vector of alteration types.
56 
+
57 
+Since different alteration types may be drawn into one same grid in the heatmap, we need to define
58 
+graphic function to add the graphics. Here if the graphics have no transparency, orders of how to add
59 
+graphics matters. In following example, snv are first drawn and then the indel. You can see rectangles
60 
+for indels are actually smaller than that for snvs so that you can visualiza both snvs and indels if they
61 
+are in a same grid.
62 
+
63 
+For the self-defined graphic function, there should be four arguments which are positions of the grids
64 
+on the heatmap (`x` and `y`), and widths and heights of the grids (`w` and `h`).
65 
+
66 
+Colors for different alterations are defined in `col`. It should be a named vector for which names correspond
67 
+to alteration types.
68 
+
69 
+
70 
+```{r}
71 
+oncoPrint(mat, get_type = function(x) strsplit(x, ";")[[1]],
72 
+	alter_fun_list = list(
73 
+		snv = function(x, y, w, h) grid.rect(x, y, w*0.9, h*0.9, gp = gpar(fill = "red", col = NA)),
74 
+		indel = function(x, y, w, h) grid.rect(x, y, w*0.9, h*0.4, gp = gpar(fill = "blue", col = NA))
75 
+	), col = c(snv = "red", indel = "blue"))
76 
+```
77 
+
78 
+The second type of input data is a list of matrix for which each matrix contains binary value representing
79 
+whether the alteration is absent or present. The list should have names and the name corresponds to the alteration
80 
+types.
81 
+
82 
+```{r}
83 
+mat_list = list(snv = matrix(c(1, 0, 1, 1, 1, 0, 0, 1, 1), nrow = 3),
84 
+	            indel = matrix(c(1, 0, 0, 0, 1, 0, 1, 0, 1), nrow = 3))
85 
+rownames(mat_list$snv) = rownames(mat_list$indel) = c("g1", "g2", "g3")
86 
+colnames(mat_list$snv) = colnames(mat_list$indel) = c("s1", "s2", "s3")
87 
+mat_list
88 
+```
89 
+
90 
+Same as the first example, but here we define `background` in `alter_fun_list` argument. This function defines
91 
+how to add graphics when there is no alteration.
92 
+
93 
+```{r}
94 
+oncoPrint(mat_list,
95 
+	alter_fun_list = list(
96 
+		background = function(x, y, w, h) NULL,
97 
+		snv = function(x, y, w, h) grid.rect(x, y, w*0.9, h*0.9, gp = gpar(fill = "red", col = NA)),
98 
+		indel = function(x, y, w, h) grid.rect(x, y, w*0.9, h*0.4, gp = gpar(fill = "blue", col = NA))
99 
+	), col = c(snv = "red", indel = "blue"))
100 
+```
101 
+
102 
+Now we make an oncoPrint with a real-world data. The data is retrieved from [cBioPortal](http://www.cbioportal.org/).
103 
+Steps for getting the data are as follows:
104 
+
105 
+1. go to http://www.cbioportal.org
106 
+2. search Cancer Study: "Lung Adenocarcinoma Carcinoma" and select: "Lung Adenocarcinoma Carcinoma (TCGA, Provisinal)"
107 
+3. In "Enter Gene Set" field, select: "General: Ras-Raf-MEK-Erk/JNK signaling (26 genes)"
108 
+4. submit the form
109 
+
110 
+In the results page,
111 
+
112 
+5. go to "Download" tab, download text in "Type of Genetic alterations across all cases"
113 
+
114 
+The order of samples can also be downloaded from the results page,
115 
+
116 
+6. go to "OncoPrint" tab, move the mouse above the plot, click "download" icon and click "Sample order"
117 
+
118 
+First we read the data and do some pre-processing.
119 
+
120 
+```{r}
121 
+mat = read.table(paste0(system.file("extdata", package = "ComplexHeatmap"),
122 
+	"/tcga_lung_adenocarcinoma_provisional_ras_raf_mek_jnk_signalling.txt"),
123 
+	header = TRUE,stringsAsFactors=FALSE, sep = "\t")
124 
+mat[is.na(mat)] = ""
125 
+rownames(mat) = mat[, 1]
126 
+mat = mat[, -1]
127 
+mat=  mat[, -ncol(mat)]
128 
+mat = t(as.matrix(mat))
129 
+```
130 
+
131 
+We can adjust the order of the matrix. Here cbioPortal also provides sample orders:
132 
+
133 
+```{r}
134 
+sample_order = scan(paste0(system.file("extdata", package = "ComplexHeatmap"),
135 
+    "/sample_order.txt"), what = "character")
136 
+mat = mat[, sample_order]
137 
+```
138 
+
139 
+There are three different alterations in `mat`: `HOMDEL`, `AMP` and `MUT`. We first
140 
+define how to add graphics to correspond to different alterations.
141 
+
142 
+```{r}
143 
+alter_fun_list = list(
144 
+	background = function(x, y, w, h) {
145 
+		grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = gpar(fill = "#CCCCCC", col = NA))
146 
+	},
147 
+	HOMDEL = function(x, y, w, h) {
148 
+		grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = gpar(fill = "blue", col = NA))
149 
+	},
150 
+	AMP = function(x, y, w, h) {
151 
+		grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = gpar(fill = "red", col = NA))
152 
+	},
153 
+	MUT = function(x, y, w, h) {
154 
+		grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = gpar(fill = "#008000", col = NA))
155 
+	}
156 
+)
157 
+```
158 
+
159 
+Also colors for different alterations which will be used for barplots.
160 
+
161 
+```{r}
162 
+col = c("MUT" = "#008000", "AMP" = "red", "HOMDEL" = "blue")
163 
+```
164 
+
165 
+Make the oncoPrint and adjust heatmap components such as the title and the legend.
166 
+
167 
+```{r, fig.width = 12, fig.height = 8}
168 
+oncoPrint(mat, get_type = function(x) strsplit(x, ";")[[1]],
169 
+	alter_fun_list = alter_fun_list, col = col,
170 
+	column_title = "OncoPrint for TCGA Lung Adenocarcinoma, genes in Ras Raf MEK JNK signalling",
171 
+	heatmap_legend_param = list(title = "Alternations", at = c("AMP", "HOMDEL", "MUT"),
172 
+		labels = c("Amplification", "Deep deletion", "Mutation")))
173 
+```
174 
+
175 
+`oncoPrint()` actually returns a `HeatmapList` object, so you can add more Heatmaps or row annotations
176 
+to it to visualize more complicated information.
177 
+
178 
+Following example splits the heatmap into two halves and add a new heatmap to the right.
179 
+
180 
+```{r, fig.width = 12, fig.height = 8}
181 
+ht_list = oncoPrint(mat, get_type = function(x) strsplit(x, ";")[[1]],
182 
+	alter_fun_list = alter_fun_list, col = col,
183 
+	column_title = "OncoPrint for TCGA Lung Adenocarcinoma, genes in Ras Raf MEK JNK signalling",
184 
+	heatmap_legend_param = list(title = "Alternations", at = c("AMP", "HOMDEL", "MUT"),
185 
+		labels = c("Amplification", "Deep deletion", "Mutation")),
186 
+	split = sample(letters[1:2], nrow(mat), replace = TRUE)) +
187 
+Heatmap(matrix(rnorm(nrow(mat)*10), ncol = 10), width = unit(4, "cm"))
188 
+draw(ht_list, row_sub_title_side = "left")
189 
+```