@@ -5,6 +5,7 @@

 # == param

 # -x a vector of numeric values.

 # -which is the annotation a column annotation or a row annotation?

+# -border whether show border of the annotation compoment

 # -gp graphic parameters.

 # -pch point type.

 # -size point size.

@@ -20,7 +21,7 @@

 # == author

 # Zuguang Gu <z.gu@dkfz.de>

 #

-anno_points = function(x, which = c("column", "row"), gp = gpar(), pch = 16, 

+anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16, 

 	size = unit(2, "mm"), axis = FALSE, axis_side = NULL, 

 	axis_gp = gpar(fontsize = 8), ...) {

@@ -54,7 +55,7 @@ anno_points = function(x, which = c("column", "row"), gp = gpar(), pch = 16,

 			}

 			pushViewport(viewport(xscale = data_scale, yscale = c(0.5, n+0.5)))

-			grid.rect()

+			if(border) grid.rect()

 			grid.points(x[index], n - seq_along(index) + 1, gp = gp, default.units = "native", pch = pch, size = size)

 			if(axis) {

 				if(k == 1 && axis_side == "top") {

@@ -70,7 +71,7 @@ anno_points = function(x, which = c("column", "row"), gp = gpar(), pch = 16,

 			gp = subset_gp(gp, index)

 			pushViewport(viewport(xscale = c(0.5, n+0.5), yscale = data_scale))

-			grid.rect()

+			if(border) grid.rect()

 			grid.points(seq_along(index), x[index], gp = gp, default.units = "native", pch = pch, size = size)

 			if(axis) {

 				if(axis_side == "left") {

@@ -89,6 +90,8 @@ anno_points = function(x, which = c("column", "row"), gp = gpar(), pch = 16,

 # == param

 # -x a vector of numeric values.

 # -which is the annotation a column annotation or a row annotation?

+# -border whether show border of the annotation compoment

+# -bar_width relative width of the bars, should less than one

 # -gp graphic parameters.

 # -axis whether add axis

 # -axis_side if it is placed as column annotation, value can only be "left" or "right".

@@ -102,14 +105,14 @@ anno_points = function(x, which = c("column", "row"), gp = gpar(), pch = 16,

 # == author

 # Zuguang Gu <z.gu@dkfz.de>

 #

-anno_barplot = function(x, which = c("column", "row"), 

+anno_barplot = function(x, which = c("column", "row"), border = TRUE, bar_width = 0.6,

 	gp = gpar(fill = "#CCCCCC"), axis = FALSE, axis_side = NULL, 

 	axis_gp = gpar(fontsize = 8), ...) {

 	x = x

 	which = match.arg(which)[1]

-	factor = 0.6

+	factor = bar_width

 	data_scale = range(x)

 	data_scale = data_scale + c(-0.05, 0.05)*(data_scale[2] - data_scale[1])

 	gp = check_gp(gp)

@@ -138,7 +141,7 @@ anno_barplot = function(x, which = c("column", "row"),

 			}

 			pushViewport(viewport(xscale = data_scale, yscale = c(0.5, n+0.5)))

-			grid.rect()

+			if(border) grid.rect()

 			grid.rect(x = data_scale[1], y = n - seq_along(index) + 1, width = x[index] - data_scale[1], height = 1*factor, just = "left", default.units = "native", gp = gp)

 			if(axis) {

 				if(k == 1 && axis_side == "top") {

@@ -155,7 +158,7 @@ anno_barplot = function(x, which = c("column", "row"),

 			gp = subset_gp(gp, index)

 			pushViewport(viewport(xscale = c(0.5, n+0.5), yscale = data_scale))

-			grid.rect()

+			if(border) grid.rect()

 			grid.rect(x = seq_along(index), y = data_scale[1], height = x[index] - data_scale[1], width = 1*factor, just = "bottom", default.units = "native", gp = gp)

 			if(axis) {

 				if(axis_side == "left") {

@@ -175,6 +178,7 @@ anno_barplot = function(x, which = c("column", "row"),

 # -x a matrix or a list. If ``x`` is a matrix and if ``which`` is ``column``, statistics for boxplot

 #    is calculated by columns, if ``which`` is ``row``, the calculation is by rows.

 # -which is the annotation a column annotation or a row annotation?

+# -border whether show border of the annotation compoment

 # -gp graphic parameters

 # -pch point type

 # -size point size

@@ -189,7 +193,8 @@ anno_barplot = function(x, which = c("column", "row"),

 # == author

 # Zuguang Gu <z.gu@dkfz.de>

 #

-anno_boxplot = function(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"), 

+anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

+	gp = gpar(fill = "#CCCCCC"), 

 	pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL, 

 	axis_gp = gpar(fontsize = 8)) {

@@ -234,7 +239,7 @@ anno_boxplot = function(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC

 				stop(paste0("Length of index should be ", ncol(boxplot_stats)))

 			}

 			pushViewport(viewport(xscale = data_scale, yscale = c(0.5, n+0.5)))

-			grid.rect()

+			if(border) grid.rect()

 			grid.segments(boxplot_stats[5, ], n - seq_along(index) + 1 - 0.5*factor, 

 				          boxplot_stats[5, ], n - seq_along(index) + 1 + 0.5*factor, default.units = "native", gp = gp)

 			grid.segments(boxplot_stats[5, ], n - seq_along(index) + 1,

@@ -271,7 +276,7 @@ anno_boxplot = function(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC

 				stop(paste0("Length of index should be ", ncol(boxplot_stats)))

 			}

 			pushViewport(viewport(xscale = c(0.5, n+0.5), yscale = data_scale))

-			grid.rect()

+			if(border) grid.rect()

 			grid.segments(seq_along(index) - 0.5*factor, boxplot_stats[5, ],

 				          seq_along(index) + 0.5*factor, boxplot_stats[5, ], default.units = "native", gp = gp)

 			grid.segments(seq_along(index), boxplot_stats[5, ],

new file mode 100644

Binary files /dev/null and b/inst/extdata/measles.rds differ

@@ -21,5 +21,6 @@ It is only designed for \code{+} generic method so that above three classes can

+

 # no example

 NULL}

@@ -33,5 +33,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example

 NULL}

@@ -36,5 +36,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # for examples, please go to `ColorMapping` method page

 NULL}

@@ -44,6 +44,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # discrete color mapping for characters

 cm = ColorMapping(name = "test",

     colors = c("blue", "white", "red"),

@@ -78,5 +78,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # for examples, please go to `Heatmap` method page

 NULL}

@@ -128,6 +128,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -35,5 +35,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # for examples, please go to `HeatmapAnnotation` method page

 NULL}

@@ -54,6 +54,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = HeatmapAnnotation(df = df)

@@ -74,6 +74,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -33,6 +33,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 There is no public constructor method for the \code{\link{HeatmapList-class}}.}

 \examples{

@@ -41,5 +42,6 @@ There is no public constructor method for the \code{\link{HeatmapList-class}}.}

+

 # no example

 NULL}

@@ -45,5 +45,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # for examples, please go to `SingleAnnotation` method page

 NULL}

@@ -55,6 +55,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # discrete character

 SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))

 SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"), 

@@ -37,6 +37,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -9,13 +9,15 @@ Using barplot as annotation

 }

 \usage{

-anno_barplot(x, which = c("column", "row"),

+anno_barplot(x, which = c("column", "row"), border = TRUE, bar_width = 0.6,

     gp = gpar(fill = "#CCCCCC"), axis = FALSE, axis_side = NULL,

     axis_gp = gpar(fontsize = 8), ...)}

 \arguments{

   \item{x}{a vector of numeric values.}

   \item{which}{is the annotation a column annotation or a row annotation?}

+  \item{border}{whether show border of the annotation compoment}

+  \item{bar_width}{relative width of the bars, should less than one}

   \item{gp}{graphic parameters.}

   \item{axis}{whether add axis}

   \item{axis_side}{if it is placed as column annotation, value can only be "left" or "right".If it is placed as row annotation, value can only be "bottom" or "top".}

@@ -37,6 +39,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 f = anno_barplot(rnorm(10))

 grid.newpage(); f(1:10)

@@ -9,13 +9,15 @@ Using boxplot as annotation

 }

 \usage{

-anno_boxplot(x, which = c("column", "row"), gp = gpar(fill = "#CCCCCC"),

+anno_boxplot(x, which = c("column", "row"), border = TRUE,

+    gp = gpar(fill = "#CCCCCC"),

     pch = 16, size = unit(2, "mm"), axis = FALSE, axis_side = NULL,

     axis_gp = gpar(fontsize = 8))}

 \arguments{

   \item{x}{a matrix or a list. If \code{x} is a matrix and if \code{which} is \code{column}, statistics for boxplotis calculated by columns, if \code{which} is \code{row}, the calculation is by rows.}

   \item{which}{is the annotation a column annotation or a row annotation?}

+  \item{border}{whether show border of the annotation compoment}

   \item{gp}{graphic parameters}

   \item{pch}{point type}

   \item{size}{point size}

@@ -38,6 +40,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(32), nrow = 4)

 f = anno_boxplot(mat)

 grid.newpage(); f(1:8)

@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(32), nrow = 4)

 f = anno_density(mat)

 grid.newpage(); f(1:8)

@@ -32,6 +32,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(32), nrow = 4)

 f = anno_histogram(mat)

 grid.newpage(); f(1:8)

@@ -9,13 +9,14 @@ Using points as annotation

 }

 \usage{

-anno_points(x, which = c("column", "row"), gp = gpar(), pch = 16,

+anno_points(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16,

     size = unit(2, "mm"), axis = FALSE, axis_side = NULL,

     axis_gp = gpar(fontsize = 8), ...)}

 \arguments{

   \item{x}{a vector of numeric values.}

   \item{which}{is the annotation a column annotation or a row annotation?}

+  \item{border}{whether show border of the annotation compoment}

   \item{gp}{graphic parameters.}

   \item{pch}{point type.}

   \item{size}{point size.}

@@ -39,5 +40,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 f = anno_points(rnorm(10))

 grid.newpage(); f(1:10)}

@@ -35,6 +35,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(100), 10)

 colnames(mat) = letters[1:10]

 rownames(mat) = LETTERS[1:10]

@@ -39,5 +39,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -44,6 +44,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # discrete color mapping for characters

 cm = ColorMapping(name = "test",

     colors = c("blue", "white", "red"),

@@ -37,5 +37,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = rowAnnotation(df = df)}

@@ -34,4 +34,5 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method}

@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method}

@@ -26,6 +26,7 @@ This function is only for internal use.

+

 This function is only for internal use.}

 \value{

 A \code{\link[grid]{unit}} object.

@@ -42,4 +43,5 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method}

@@ -34,4 +34,5 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method}

@@ -36,6 +36,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(40), nr = 4, ncol = 10)

 rownames(mat) = letters[1:4]

 colnames(mat) = letters[1:10]

@@ -37,6 +37,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -37,6 +37,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = HeatmapAnnotation(df = df)

 grid.newpage(); draw(ha, 1:6)

@@ -40,6 +40,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -38,6 +38,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 anno = SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))

 grid.newpage(); draw(anno, 1:5)

 grid.newpage(); draw(anno, c(1, 4, 3, 5, 2))

@@ -40,5 +40,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -38,5 +38,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -41,5 +41,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -48,5 +48,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -42,5 +42,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -38,5 +38,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -36,5 +36,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -39,5 +39,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -37,5 +37,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -36,5 +36,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -40,6 +40,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 hc = hclust(dist(USArrests[1:5, ]))

 dend = as.dendrogram(hc)

@@ -36,5 +36,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -36,5 +36,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -39,5 +39,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -65,5 +65,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -38,5 +38,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -35,6 +35,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # discrete color mapping for characters

 cm = ColorMapping(name = "test",

     colors = c("blue", "white", "red"),

@@ -53,6 +53,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 df = data.frame(matrix(rnorm(40), nrow = 10, dimnames = list(letters[1:10], letters[1:4])),

                 large = runif(10)*100,

                 t1 = sample(letters[1:3], 10, replace = TRUE),

@@ -43,5 +43,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -37,5 +37,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 df = data.frame(type = c("a", "a", "a", "b", "b", "b"))

 ha = columnAnnotation(df = df)}

@@ -36,5 +36,6 @@ Zuguang Gu <z.gu@dkfz.de>

+

 # no example for this internal method

 NULL}

@@ -34,6 +34,7 @@ Zuguang Gu <z.gu@dkfz.de>

+

 mat = matrix(rnorm(80, 2), 8, 10)

 mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))

 rownames(mat) = letters[1:12]

@@ -30,4 +30,5 @@ This function returns no value.

+

 Zuguang Gu <z.gu@dkfz.de>}

@@ -83,3 +83,18 @@ for colors for continous values.

 Heatmap(mat, col = topo.colors(50), row_hclust_width = unit(2, "cm"), 

     column_hclust_height = unit(2, "cm"))

 ```

+

+```

+mat = readRDS(paste0(system.files("extdata", package = "ComplexHeatmap"), "/measles.RData"))

+ha = HeatmapAnnotation(dist = anno_barplot(colSums(mat)))

+Heatmap(mat, name = "mat", col = colorRamp2(c(0, 800, 1000, 127000), c("white", "cornflowerblue", "yellow", "red")),

+    cluster_columns = FALSE, show_row_hclust = FALSE, rect_gp = gpar(col= "white"),

+    column_title = 'Measles cases in US states 1930-2001\nVaccine introduced 1961\n(data from Project Tycho)',

+    top_annotation = ha, top_annotation_height = unit(4, "cm"))

+

+decorate_heatmap_body("mat", {

+    i = which(yd$year == 1961)

+    x = i/ncol(mat)

+    grid.lines(c(x, x), c(0, 1), gp = gpar(lty = 2, lwd = 2))

+})

+```

\ No newline at end of file