1. ComplexHeatmap
  2. tests_not_run
  3. test-AnnotationFunction.R
Browse code

add unit_to_numeric() function

jokergoo authored on 05/03/2020 14:31:53
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
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-
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-normalize_graphic_param_to_mat(1, nc = 2, nr = 4, "foo")
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-normalize_graphic_param_to_mat(1:2, nc = 2, nr = 4, "foo")
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-normalize_graphic_param_to_mat(1:4, nc = 2, nr = 4, "foo")
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-
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-### AnnotationFunction constructor #####
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-fun = function(index) {
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-	x = runif(10)
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-	pushViewport(viewport(xscale = c(0.5, 10.5), yscale = c(0, 1)))
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-	grid.points(index, x[index])
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-	popViewport()
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-}
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-anno = AnnotationFunction(fun = fun)
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-
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-x = runif(10)
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-fun = function(index) {
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-	pushViewport(viewport(xscale = c(0.5, 10.5), yscale = c(0, 1)))
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-	grid.points(index, x[index])
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-	popViewport()
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-}
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-anno = AnnotationFunction(fun = fun, var_imported = "x")
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-anno = AnnotationFunction(fun = fun, var_imported = list(x))
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-
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-
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-devAskNewPage(ask = TRUE)
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-
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-########### testing anno_simple ############
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-anno = anno_simple(1:10)
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-draw(anno, test = "as a simple vector")
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-draw(anno[1:5], test = "subset of column annotation")
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-anno = anno_simple(1:10, which = "row")
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-draw(anno, test = "as row annotation")
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-draw(anno[1:5], test = "subste of row annotation")
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-
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-anno = anno_simple(1:10, col = structure(rand_color(10), names = 1:10))
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-draw(anno, test = "self-define colors")
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-
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-anno = anno_simple(1:10, border = TRUE)
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-draw(anno, test = "border")
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-anno = anno_simple(1:10, gp = gpar(col = "red"))
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-draw(anno, test = "gp for the grids")
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-
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-anno = anno_simple(c(1:9, NA))
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-draw(anno, test = "vector has NA values")
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-
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-anno = anno_simple(cbind(1:10, 10:1))
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-draw(anno, test = "a matrix")
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-draw(anno[1:5], test = "subste of a matrix")
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-
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-anno = anno_simple(1:10, pch = 1, pt_gp = gpar(col = "red"), pt_size = unit(seq(1, 10), "mm"))
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-draw(anno, test = "with symbols + pt_gp + pt_size")
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-anno = anno_simple(1:10, pch = 1:10)
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-draw(anno, test = "pch is a vector")
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-anno = anno_simple(1:10, pch = c(1:4, NA, 6:8, NA, 10, 11))
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-draw(anno, test = "pch has NA values")
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-
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-anno = anno_simple(cbind(1:10, 10:1), pch = 1, pt_gp = gpar(col = "blue"))
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-draw(anno, test = "matrix with symbols")
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-anno = anno_simple(cbind(1:10, 10:1), pch = 1:2)
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-draw(anno, test = "matrix, length of pch is number of annotations")
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-anno = anno_simple(cbind(1:10, 10:1), pch = 1:10)
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-draw(anno, test = "matrix, length of pch is length of samples")
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-anno = anno_simple(cbind(1:10, 10:1), pch = matrix(1:20, nc = 2))
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-draw(anno, test = "matrix, pch is a matrix")
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-pch = matrix(1:20, nc = 2)
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-pch[sample(length(pch), 10)] = NA
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-anno = anno_simple(cbind(1:10, 10:1), pch = pch)
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-draw(anno, test = "matrix, pch is a matrix with NA values")
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-
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-
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-####### test anno_empty ######
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-anno = anno_empty()
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-draw(anno, test = "anno_empty")
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-anno = anno_empty(border = FALSE)
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-draw(anno, test = "anno_empty without border")
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-
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-###### test anno_image #####
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-image1 = sample(dir("~/Downloads/IcoMoon-Free-master/PNG/64px", full.names = TRUE), 10)
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-anno = anno_image(image1)
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-draw(anno, test = "png")
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-draw(anno[1:5], test = "subset of png")
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-anno = anno_image(image1, which = "row")
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-draw(anno, test = "png on rows")
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-image2 = sample(dir("~/Downloads/IcoMoon-Free-master/SVG/", full.names = TRUE), 10)
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-anno = anno_image(image2)
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-draw(anno, test = "svg")
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-image3 = sample(dir("~/Downloads/IcoMoon-Free-master/EPS/", full.names = TRUE), 10)
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-anno = anno_image(image3)
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-draw(anno, test = "eps")
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-image4 = sample(dir("~/Downloads/IcoMoon-Free-master/PDF/", full.names = TRUE), 10)
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-anno = anno_image(image4)
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-draw(anno, test = "pdf")
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-
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-anno = anno_image(c(image1[1:3], image2[1:3], image3[1:3], image4[1:3]))
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-draw(anno, test = "png+svg+eps+pdf")
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-
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-anno = anno_image(image1, gp = gpar(fill = 1:10, col = "black"))
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-draw(anno, test = "png + gp")
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-draw(anno[1:5], test = "png + gp")
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-
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-anno = anno_image(image1, space = unit(3, "mm"))
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-draw(anno, test = "space")
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-
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-image1[1] = ""
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-anno = anno_image(image1)
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-draw(anno, test = "png")
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-
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-######## test anno_points #####
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-anno = anno_points(runif(10))
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-draw(anno, test = "anno_points")
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-anno = anno_points(matrix(runif(20), nc = 2), pch = 1:2)
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-draw(anno, test = "matrix")
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-anno = anno_points(c(1:5, 1:5))
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-draw(anno, test = "anno_points")
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-anno = anno_points(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3))
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-draw(anno, test = "matrix")
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-
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-anno = anno_points(1:10, gp = gpar(col = rep(2:3, each = 5)), pch = rep(2:3, each = 5))
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-draw(anno, test = "anno_points")
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-draw(anno, index = c(1, 3, 5, 7, 9, 2, 4, 6, 8, 10), test = "anno_points")
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-
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-anno = anno_points(c(1:5, NA, 7:10))
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-draw(anno, test = "anno_points")
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-
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-
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-anno = anno_points(runif(10), axis_param = list(direction = "reverse"), ylim = c(0, 1))
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-draw(anno, test = "anno_points")
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-
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-anno = anno_points(runif(10), axis_param = list(direction = "reverse"), ylim = c(0, 1), which = "row")
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-draw(anno, test = "anno_points")
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-
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-# pch as image
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-image1 = sample(dir("/desktop-home/guz/Downloads/IcoMoon-Free-master/PNG/64px", full.names = TRUE), 10)
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-x = runif(10)
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-anno1 = anno_points(x, pch = image1, pch_as_image = TRUE, size = unit(5, "mm"), height = unit(4, "cm"))
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-anno2 = anno_points(x, height = unit(4, "cm"))
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-draw(anno1, test = "anno_points")
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-draw(anno2, test = "anno_points")
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-
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-##### test anno_lines ###
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-anno = anno_lines(runif(10))
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-draw(anno, test = "anno_lines")
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-anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3))
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-draw(anno, test = "matrix")
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-anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3),
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-	add_points = TRUE, pt_gp = gpar(col = 5:6), pch = c(1, 16))
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-draw(anno, test = "matrix")
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-anno = anno_lines(sort(rnorm(10)), height = unit(2, "cm"), smooth = TRUE, add_points = TRUE)
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-draw(anno, test = "anno_lines, smooth")
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-anno = anno_lines(cbind(sort(rnorm(10)), sort(rnorm(10), decreasing = TRUE)),
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-	height = unit(2, "cm"), smooth = TRUE, add_points = TRUE, gp = gpar(col = 2:3))
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-draw(anno, test = "anno_lines, smooth, matrix")
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-
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-anno = anno_lines(sort(rnorm(10)), width = unit(2, "cm"), smooth = TRUE, add_points = TRUE, which = "row")
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-draw(anno, test = "anno_lines, smooth, by row")
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-anno = anno_lines(cbind(sort(rnorm(10)), sort(rnorm(10), decreasing = TRUE)),
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-	width = unit(2, "cm"), smooth = TRUE, add_points = TRUE, gp = gpar(col = 2:3), which = "row")
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-draw(anno, test = "anno_lines, smooth, matrix, by row")
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-
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-anno = anno_lines(c(1:5, NA, 7:10))
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-draw(anno, test = "anno_lines")
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-
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-anno = anno_lines(runif(10), axis_param = list(direction = "reverse"))
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-draw(anno, test = "anno_lines")
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-
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-###### test anno_text #######
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-anno = anno_text(month.name)
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-draw(anno, test = "month names")
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-anno = anno_text(month.name, gp = gpar(fontsize = 16))
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-draw(anno, test = "month names with fontsize")
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-anno = anno_text(month.name, gp = gpar(fontsize = 1:12+4))
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-draw(anno, test = "month names with changing fontsize")
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-anno = anno_text(month.name, which = "row")
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-draw(anno, test = "month names on rows")
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-anno = anno_text(month.name, location = 0, rot = 45, just = "left", gp = gpar(col = 1:12))
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-draw(anno, test = "with rotations")
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-anno = anno_text(month.name, location = 1, rot = 45, just = "right", gp = gpar(fontsize = 1:12+4))
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-draw(anno, test = "with rotations")
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-
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-devAskNewPage(ask = TRUE)
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-for(rot in seq(0, 360, by = 45)) {
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-	anno = anno_text(month.name, which = "row", location = 0, rot = rot,
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-		just = "left")
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-	draw(anno, test = paste0("rot =", rot))
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-}
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-
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-
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-##### test anno_barplot #####
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-anno = anno_barplot(1:10)
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-draw(anno, test = "a vector")
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-draw(anno[1:5], test = "a vector, subset")
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-anno = anno_barplot(1:10, which = "row")
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-draw(anno, test = "a vector")
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-anno = anno_barplot(1:10, bar_width = 1)
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-draw(anno, test = "bar_width")
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-anno = anno_barplot(1:10, gp = gpar(fill = 1:10))
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-draw(anno, test = "fill colors")
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-
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-anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)))
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-draw(anno, test = "a matrix")
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-draw(anno[1:5], test = "a matrix, subset")
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-anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), which = "row")
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-draw(anno, test = "a matrix, on rows")
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-anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), gp = gpar(fill = 2:3, col = 2:3))
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-draw(anno, test = "a matrix with fill")
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-
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-m = matrix(runif(4*10), nc = 4)
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-m = t(apply(m, 1, function(x) x/sum(x)))
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-anno = anno_barplot(m)
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-draw(anno, test = "proportion matrix")
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-anno = anno_barplot(m, gp = gpar(fill = 2:5), bar_width = 1, height = unit(6, "cm"))
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-draw(anno, test = "proportion matrix")
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-
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-anno = anno_barplot(c(1:5, NA, 7:10))
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-draw(anno, test = "a vector")
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-
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-anno = anno_barplot(1:10, which = "row", axis_param = list(direction = "reverse"))
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-draw(anno, test = "a vector")
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-
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-anno = anno_barplot(1:10, baseline = 5, which = "row", axis_param = list(direction = "reverse"))
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-draw(anno, test = "a vector")
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-
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-anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), which = "row", axis_param = list(direction = "reverse"))
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-draw(anno, test = "a vector")
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-
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-
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-##### test anno_boxplot #####
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-set.seed(123)
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-m = matrix(rnorm(100), 10)
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-anno = anno_boxplot(m, height = unit(4, "cm"))
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-draw(anno, test = "anno_boxplot")
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-draw(anno[1:5], test = "subset")
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-anno = anno_boxplot(m, height = unit(4, "cm"), gp = gpar(fill = 1:10))
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-draw(anno, test = "anno_boxplot with gp")
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-anno = anno_boxplot(m, height = unit(4, "cm"), box_width = 0.9)
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-draw(anno, test = "anno_boxplot with box_width")
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-
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-m = matrix(rnorm(100), 10)
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-m[1, ] = NA
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-anno = anno_boxplot(m, height = unit(4, "cm"))
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-draw(anno, test = "anno_boxplot")
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-
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-
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-####### test anno_joyplot ####
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-m = matrix(rnorm(1000), nc = 10)
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-lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")]))
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-anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row")
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-draw(anno, test = "joyplot")
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-anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", gp = gpar(fill = 1:10))
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-draw(anno, test = "joyplot + col")
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-anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", scale = 1)
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-draw(anno, test = "joyplot + scale")
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-
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-m = matrix(rnorm(5000), nc = 50)
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-lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")]))
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-anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", gp = gpar(fill = NA), scale = 4)
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-draw(anno, test = "joyplot")
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-
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-######## test anno_horizon ######
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-lt = lapply(1:20, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1)
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-anno = anno_horizon(lt, which = "row")
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-draw(anno, test = "horizon chart")
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-anno = anno_horizon(lt, which = "row", gp = gpar(pos_fill = "orange", neg_fill = "darkgreen"))
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-draw(anno, test = "horizon chart, col")
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-anno = anno_horizon(lt, which = "row", negative_from_top = TRUE)
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-draw(anno, test = "horizon chart + negative_from_top")
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-anno = anno_horizon(lt, which = "row", gap = unit(1, "mm"))
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-draw(anno, test = "horizon chart + gap")
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-anno = anno_horizon(lt, which = "row", gp = gpar(pos_fill = rep(c("orange", "red"), each = 10),
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-	neg_fill = rep(c("darkgreen", "blue"), each = 10)))
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-draw(anno, test = "horizon chart, col")
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-
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-####### test anno_histogram ####
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-m = matrix(rnorm(1000), nc = 10)
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-anno = anno_histogram(t(m), which = "row")
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-draw(anno, test = "row histogram")
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-draw(anno[1:5], test = "subset row histogram")
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-anno = anno_histogram(t(m), which = "row", gp = gpar(fill = 1:10))
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-draw(anno, test = "row histogram with color")
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-anno = anno_histogram(t(m), which = "row", n_breaks = 20)
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-draw(anno, test = "row histogram with color")
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-m[1, ] = NA
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-anno = anno_histogram(t(m), which = "row")
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-draw(anno, test = "row histogram")
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-
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-
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-####### test anno_density ######
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-anno = anno_density(t(m), which = "row")
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-draw(anno, test = "normal density")
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-draw(anno[1:5], test = "normal density, subset")
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-anno = anno_density(t(m), which = "row", type = "violin")
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-draw(anno, test = "violin")
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-anno = anno_density(t(m), which = "row", type = "heatmap")
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-draw(anno, test = "heatmap")
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-anno = anno_density(t(m), which = "row", type = "heatmap", heatmap_colors = c("white", "orange"))
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-draw(anno, test = "heatmap, colors")
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-
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-
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-###### anno_mark ###
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-library(gridtext)
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-grid.text = function(text, x = 0.5, y = 0.5, gp = gpar(), rot = 0, default.units = "npc", just = "center") {
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-	if(length(just) == 1) {
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-		if(just == "center") {
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-			just = c("center", "center")
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-		} else if(just == "bottom") {
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-			just = c("center", "bottom")
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-		} else if (just == "top") {
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-			just = c("center", "top")
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-		} else if(just == "left") {
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-			just = c("left", "center")
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-		} else if(just == "right") {
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-			just = c("right", "center")
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-		}
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-	}
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-	just2 = c(0.5, 0.5)
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-	if(is.character(just)) {
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-		just2[1] = switch(just[1], "center" = 0.5, "left" = 0, "right" = 1)
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-		just2[2] = switch(just[2], "center" = 0.5, "bottom" = 0, "top" = 1)
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-	}
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-	gb = richtext_grob(text, x = x, y = y, gp = gpar(fontsize = 10), box_gp = gpar(col = "black"),
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-		default.units = default.units, hjust = just2[1], vjust = just2[2], rot = rot)
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-	grid.draw(gb)
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-}
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-
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-anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
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-draw(anno, index = 1:100, test = "anno_mark")
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-
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-anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], labels_rot = 30, which = "column")
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-draw(anno, index = 1:100, test = "anno_mark")
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-
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-m = matrix(1:1000, byrow = TRUE, nr = 100)
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-anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row", labels_rot = 30)
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-Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)
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-Heatmap(m) + rowAnnotation(mark = anno)
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-
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-ht_list = Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)
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-draw(ht_list, row_split = c(rep("a", 95), rep("b", 5)))
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-
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-
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-grid.newpage()
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-pushViewport(viewport(x = 0.45, w = 0.7, h = 0.95))
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-h = unit(0, "mm")
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-for(rot in seq(0, 360, by = 30)[-13]) {
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-	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = strrep(letters[1:10], 4), labels_rot = rot, which = "column", side = "bottom")
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-	h = h + height(anno)
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-	pushViewport(viewport(y = h, height = height(anno), just = "top"))
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-	grid.rect()
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-	draw(anno, index = 1:100)
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-	grid::grid.text(qq("labels_rot = @{rot}"), unit(1, "npc") + unit(2, "mm"), just = "left")
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-	popViewport()
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-}
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-
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-
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-grid.newpage()
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-pushViewport(viewport(w = 0.9, h = 0.9))
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-w = unit(0, "mm")
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-for(rot in seq(0, 360, by = 30)) {
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-	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = strrep(letters[1:10], 4), labels_rot = rot, which = "row", side = "left")
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-	w = w + width(anno)
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-	pushViewport(viewport(x = w, width = width(anno), just = "right"))
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-	grid.rect()
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-	draw(anno, index = 1:100)
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-	popViewport()
364 
-}
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-
366 
-
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-
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-### graphic parameters after reordering
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-index = c(1, 3, 5, 7, 9, 2, 4, 6, 8, 10)
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-anno = anno_simple(1:10, pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
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-	pt_size = unit(1:10, "mm"))
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-draw(anno, index, test = "a numeric vector")
373 
-anno = anno_simple(1:10, pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
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-	pt_size = unit(1:10, "mm"), which = "row")
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-draw(anno, index, test = "a numeric vector")
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-
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-
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-anno = anno_points(1:10, pch = 1:10, gp = gpar(col = rep(c(1, 2), each = 5)),
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-	size = unit(1:10, "mm"))
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-draw(anno, index, test = "a numeric vector")
381 
-anno = anno_points(1:10, pch = 1:10, gp = gpar(col = rep(c(1, 2), each = 5)),
382 
-	size = unit(1:10, "mm"), which = "row")
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-draw(anno, index, test = "a numeric vector")
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-
385 
-
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-anno = anno_lines(sort(runif(10)), pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
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-	size = unit(1:10, "mm"), add_points = TRUE)
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-draw(anno, index, test = "a numeric vector")
389 
-anno = anno_lines(sort(runif(10)), pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
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-	size = unit(1:10, "mm"), add_points = TRUE, which = "row")
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-draw(anno, index, test = "a numeric vector")
392 
-
393 
-
394 
-anno = anno_barplot(1:10, gp = gpar(fill = rep(c(1, 2), each = 5)))
395 
-draw(anno, index, test = "a numeric vector")
396 
-anno = anno_barplot(1:10, gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
397 
-draw(anno, index, test = "a numeric vector")
398 
-
399 
-anno = anno_barplot(cbind(1:10, 10:1), gp = gpar(fill = 1:2))
400 
-draw(anno, index, test = "a numeric vector")
401 
-anno = anno_barplot(cbind(1:10, 10:1), gp = gpar(fill = 1:2), which = "row")
402 
-draw(anno, index, test = "a numeric vector")
403 
-
404 
-
405 
-m = matrix(rnorm(100), 10)
406 
-m = m[, order(apply(m, 2, median))]
407 
-anno = anno_boxplot(m, pch = 1:10, gp = gpar(fill = rep(c(1, 2), each = 5)),
408 
-	size = unit(1:10, "mm"), height = unit(4, "cm"))
409 
-draw(anno, index, test = "a numeric vector")
410 
-anno = anno_boxplot(t(m), pch = 1:10, gp = gpar(fill = rep(c(1, 2), each = 5)),
411 
-	size = unit(1:10, "mm"), which = "row", width = unit(4, "cm"))
412 
-draw(anno, index, test = "a numeric vector")
413 
-
414 
-anno = anno_histogram(m, gp = gpar(fill = rep(c(1, 2), each = 5)))
415 
-draw(anno, index, test = "a numeric vector")
416 
-anno = anno_histogram(t(m), gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
417 
-draw(anno, index, test = "a numeric vector")
418 
-
419 
-anno = anno_density(m, gp = gpar(fill = rep(c(1, 2), each = 5)))
420 
-draw(anno, index, test = "a numeric vector")
421 
-anno = anno_density(t(m), gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
422 
-draw(anno, index, test = "a numeric vector")
423 
-
424 
-
425 
-anno = anno_density(m, type = "violin", gp = gpar(fill = rep(c(1, 2), each = 5)))
426 
-draw(anno, index, test = "a numeric vector")
427 
-anno = anno_density(t(m), type = "violin", gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
428 
-draw(anno, index, test = "a numeric vector")
429 
-
430 
-
431 
-anno = anno_text(month.name, gp = gpar(col = rep(c(1, 2), each = 5)))
432 
-draw(anno, index, test = "a numeric vector")
433 
-anno = anno_text(month.name, gp = gpar(col = rep(c(1, 2), each = 5)), which= "row")
434 
-draw(anno, index, test = "a numeric vector")
435 
-
436 
-lt = lapply(1:10, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1)
437 
-anno = anno_horizon(lt, gp = gpar(pos_fill = rep(c(1, 2), each = 5), neg_fill = rep(c(3, 4), each = 5)), which = "row")
438 
-draw(anno, index, test = "a numeric vector")
439 
-
440 
-m = matrix(rnorm(1000), nc = 10)
441 
-lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")]))
442 
-anno = anno_joyplot(lt, gp = gpar(fill = rep(c(1, 2), each = 5)),
443 
-	width = unit(4, "cm"), which = "row")
444 
-draw(anno, index, test = "joyplot")
445 
-
446 
-
447 
-anno = anno_block(gp = gpar(fill = 1:4))
448 
-draw(anno, index = 1:10, k = 1, n = 4, test = "anno_block")
449 
-draw(anno, index = 1:10, k = 2, n = 4, test = "anno_block")
450 
-
451 
-anno = anno_block(gp = gpar(fill = 1:4), labels = letters[1:4], labels_gp = gpar(col = "white"))
452 
-draw(anno, index = 1:10, k = 2, n = 4, test = "anno_block")
453 
-draw(anno, index = 1:10, k = 4, n = 4, test = "anno_block")
454 
-draw(anno, index = 1:10, k = 2, n = 2, test = "anno_block")
455 
-
456 
-anno = anno_block(gp = gpar(fill = 1:4), labels = letters[1:4], labels_gp = gpar(col = "white"), which = "row")
457 
-draw(anno, index = 1:10, k = 2, n = 4, test = "anno_block")
458 
-
459 
-
460 
-### anno_zoom
461 
-fa = sort(sample(letters[1:3], 100, replace = TRUE, prob = c(1, 2, 3)))
462 
-panel_fun = function(index, nm) {
463 
-	grid.rect()
464 
-	grid.text(nm)
465 
-}
466 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun)
467 
-draw(anno, index = 1:100, test = "anno_zoom")
468 
-
469 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
470 
-	gap = unit(1, "cm"))
471 
-draw(anno, index = 1:100, test = "anno_zoom, set gap")
472 
-
473 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
474 
-	size = 1:3)
475 
-draw(anno, index = 1:100, test = "anno_zoom, size set as relative values")
476 
-
477 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
478 
-	size = 1:3, extend = unit(1, "cm"))
479 
-draw(anno, index = 1:100, test = "anno_zoom, extend")
480 
-
481 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
482 
-	size = unit(1:3, "cm"))
483 
-draw(anno, index = 1:100, test = "anno_zoom, size set as absolute values")
484 
-
485 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
486 
-	size = unit(c(2, 20, 40), "cm"))
487 
-draw(anno, index = 1:100, test = "anno_zoom, big size")
488 
-
489 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
490 
-	size = 1:3, gap = unit(1, "cm"))
491 
-draw(anno, index = 1:100, test = "anno_zoom, size set as relative values, gap")
492 
-
493 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
494 
-	size = unit(1:3, "cm"), gap = unit(1, "cm"))
495 
-draw(anno, index = 1:100, test = "anno_zoom, size set as absolute values, gap")
496 
-
497 
-
498 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
499 
-	size = unit(1:3, "cm"), side = "left")
500 
-draw(anno, index = 1:100, test = "anno_zoom, side")
501 
-
502 
-
503 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
504 
-	size = unit(1:3, "cm"), link_gp = gpar(fill = 1:3))
505 
-draw(anno, index = 1:100, test = "anno_zoom, link_gp")
506 
-
507 
-anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
508 
-	size = unit(1:3, "cm"), link_gp = gpar(fill = 1:3),
509 
-	link_width = unit(2, "cm"), width = unit(4, "cm"))
510 
-draw(anno, index = 1:100, test = "anno_zoom, width")
511 
-
512 
-anno = anno_zoom(align_to = list(a = 1:10, b = 30:45, c = 70:90),
513 
-	which = "row", panel_fun = panel_fun, size = unit(1:3, "cm"))
514 
-draw(anno, index = 1:100, test = "anno_zoom, a list of indices")
515 
-
516 
-anno = anno_zoom(align_to = fa, which = "column", panel_fun = panel_fun,
517 
-	size = unit(1:3, "cm"))
518 
-draw(anno, index = 1:100, test = "anno_zoom, column annotation")
519 
-
520 
-
521 
-m = matrix(rnorm(100*10), nrow = 100)
522 
-hc = hclust(dist(m))
523 
-fa2 = cutree(hc, k = 4)
524 
-anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun)
525 
-draw(anno, index = hc$order, test = "anno_zoom, column annotation")
526 
-
527 
-anno = anno_zoom(align_to = fa2, which = "column", panel_fun = panel_fun)
528 
-draw(anno, index = hc$order, test = "anno_zoom, column annotation")
529 
-
530 
-
531 
-anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun)
532 
-Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno))
533 
-Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno), row_split = 2)
534 
-
535 
-
536 
-anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun, size = unit(1:4, "cm"))
537 
-Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno))
538 
-
539 
-set.seed(123)
540 
-m = matrix(rnorm(100*10), nrow = 100)
541 
-subgroup = sample(letters[1:3], 100, replace = TRUE, prob = c(1, 5, 10))
542 
-rg = range(m)
543 
-panel_fun = function(index, nm) {
544 
-	pushViewport(viewport(xscale = rg, yscale = c(0, 2)))
545 
-	grid.rect()
546 
-	grid.xaxis(gp = gpar(fontsize = 8))
547 
-	grid.boxplot(m[index, ], pos = 1, direction = "horizontal")
548 
-	grid.text(paste("distribution of group", nm), mean(rg), y = 1.9,
549 
-		just = "top", default.units = "native", gp = gpar(fontsize = 10))
550 
-	popViewport()
551 
-}
552 
-anno = anno_zoom(align_to = subgroup, which = "row", panel_fun = panel_fun,
553 
-	size = unit(2, "cm"), gap = unit(1, "cm"), width = unit(4, "cm"))
554 
-Heatmap(m, right_annotation = rowAnnotation(foo = anno), row_split = subgroup)
555 
-
556 
-panel_fun2 = function(index, nm) {
557 
-	pushViewport(viewport())
558 
-	grid.rect()
559 
-	n = floor(length(index)/4)
560 
-	txt = paste("gene function", 1:n, collapse = "\n")
561 
-	grid.text(txt, 0.95, 0.5, default.units = "npc", just = "right", gp = gpar(fontsize = 8))
562 
-	popViewport()
563 
-}
564 
-anno2 = anno_zoom(align_to = subgroup, which = "row", panel_fun = panel_fun2,
565 
-	gap = unit(1, "cm"), width = unit(3, "cm"), side = "left")
566 
-
567 
-# in infinite loop
568 
-Heatmap(m, right_annotation = rowAnnotation(subgroup = subgroup, foo = anno,
569 
-	show_annotation_name = FALSE),
570 
-	left_annotation = rowAnnotation(bar = anno2, subgroup = subgroup, show_annotation_name = FALSE),
571 
-	show_row_dend = FALSE,
572 
-	row_split = subgroup)
573 
-
574 
-Heatmap(m, right_annotation = rowAnnotation(foo = anno),
575 
-	left_annotation = rowAnnotation(bar = anno2),
576 
-	show_row_dend = FALSE,
577 
-	row_split = subgroup)
Browse code

anno_simple(): fixed a bug when all pch are NA in a slice

Zuguang Gu authored on 25/02/2020 14:51:37
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @7539e69
... ... 
@@ -184,13 +184,6 @@ for(rot in seq(0, 360, by = 45)) {
184 184 
 	draw(anno, test = paste0("rot =", rot))
185 185 
 }
186 186
187 
-##### test anno_richtext ####
188 
-anno = anno_richtext(richtext_grob(month.name, box_gp = gpar(col = "red"), rot = 90, hjust = 1, y = unit(1, "npc")))
189 
-draw(anno, test = "month names")
190 
-anno = anno_richtext(richtext_grob(month.name, box_gp = gpar(col = "red"), hjust = 0, x = unit(0, "npc")), which = "row")
191 
-draw(anno, test = "month names")
192 
-
193 
-
194 187
195 188 
 ##### test anno_barplot #####
196 189 
 anno = anno_barplot(1:10)
Browse code

support gridtext

Zuguang Gu authored on 05/02/2020 07:34:10
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @5b47a84
... ... 
@@ -184,6 +184,12 @@ for(rot in seq(0, 360, by = 45)) {
184 184 
 	draw(anno, test = paste0("rot =", rot))
185 185 
 }
186 186
187 
+##### test anno_richtext ####
188 
+anno = anno_richtext(richtext_grob(month.name, box_gp = gpar(col = "red"), rot = 90, hjust = 1, y = unit(1, "npc")))
189 
+draw(anno, test = "month names")
190 
+anno = anno_richtext(richtext_grob(month.name, box_gp = gpar(col = "red"), hjust = 0, x = unit(0, "npc")), which = "row")
191 
+draw(anno, test = "month names")
192 
+
187 193
188 194
189 195 
 ##### test anno_barplot #####
Browse code

anno_points(): images can be point symbols

jokergoo authored on 09/12/2019 11:06:42
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @260b45a
... ... 
@@ -129,6 +129,14 @@ draw(anno, test = "anno_points")
129 129 
 anno = anno_points(runif(10), axis_param = list(direction = "reverse"), ylim = c(0, 1), which = "row")
130 130 
 draw(anno, test = "anno_points")
131 131
132 
+# pch as image
133 
+image1 = sample(dir("/desktop-home/guz/Downloads/IcoMoon-Free-master/PNG/64px", full.names = TRUE), 10)
134 
+x = runif(10)
135 
+anno1 = anno_points(x, pch = image1, pch_as_image = TRUE, size = unit(5, "mm"), height = unit(4, "cm"))
136 
+anno2 = anno_points(x, height = unit(4, "cm"))
137 
+draw(anno1, test = "anno_points")
138 
+draw(anno2, test = "anno_points")
139 
+
132 140 
 ##### test anno_lines ###
133 141 
 anno = anno_lines(runif(10))
134 142 
 draw(anno, test = "anno_lines")
Browse code

text positions are correctly calculated when rotating text in anno_mark()

Zuguang Gu authored on 19/10/2019 19:52:36
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @b1e3414
... ... 
@@ -331,14 +331,15 @@ draw(ht_list, row_split = c(rep("a", 95), rep("b", 5)))
331 331
332 332
333 333 
 grid.newpage()
334 
-pushViewport(viewport(w = 0.9, h = 0.9))
334 
+pushViewport(viewport(x = 0.45, w = 0.7, h = 0.95))
335 335 
 h = unit(0, "mm")
336 
-for(rot in seq(0, 360, by = 30)) {
336 
+for(rot in seq(0, 360, by = 30)[-13]) {
337 337 
 	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = strrep(letters[1:10], 4), labels_rot = rot, which = "column", side = "bottom")
338 338 
 	h = h + height(anno)
339 339 
 	pushViewport(viewport(y = h, height = height(anno), just = "top"))
340 340 
 	grid.rect()
341 341 
 	draw(anno, index = 1:100)
342 
+	grid::grid.text(qq("labels_rot = @{rot}"), unit(1, "npc") + unit(2, "mm"), just = "left")
342 343 
 	popViewport()
343 344 
 }
344 345
Browse code

text positions are correctly calculated when rotating text in anno_mark()

Zuguang Gu authored on 19/10/2019 19:51:41
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @70c20a0
... ... 
@@ -290,6 +290,31 @@ draw(anno, test = "heatmap, colors")
290 290
291 291
292 292 
 ###### anno_mark ###
293 
+library(gridtext)
294 
+grid.text = function(text, x = 0.5, y = 0.5, gp = gpar(), rot = 0, default.units = "npc", just = "center") {
295 
+	if(length(just) == 1) {
296 
+		if(just == "center") {
297 
+			just = c("center", "center")
298 
+		} else if(just == "bottom") {
299 
+			just = c("center", "bottom")
300 
+		} else if (just == "top") {
301 
+			just = c("center", "top")
302 
+		} else if(just == "left") {
303 
+			just = c("left", "center")
304 
+		} else if(just == "right") {
305 
+			just = c("right", "center")
306 
+		}
307 
+	}
308 
+	just2 = c(0.5, 0.5)
309 
+	if(is.character(just)) {
310 
+		just2[1] = switch(just[1], "center" = 0.5, "left" = 0, "right" = 1)
311 
+		just2[2] = switch(just[2], "center" = 0.5, "bottom" = 0, "top" = 1)
312 
+	}
313 
+	gb = richtext_grob(text, x = x, y = y, gp = gpar(fontsize = 10), box_gp = gpar(col = "black"),
314 
+		default.units = default.units, hjust = just2[1], vjust = just2[2], rot = rot)
315 
+	grid.draw(gb)
316 
+}
317 
+
293 318 
 anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
294 319 
 draw(anno, index = 1:100, test = "anno_mark")
295 320
... ... 
@@ -306,10 +331,12 @@ draw(ht_list, row_split = c(rep("a", 95), rep("b", 5)))
306 331
307 332
308 333 
 grid.newpage()
309 
-pushViewport(viewport(layout = grid.layout(nrow = 12, ncol = 1)))
310 
-for(rot in seq(0, 360, by = 30)[-13]) {
334 
+pushViewport(viewport(w = 0.9, h = 0.9))
335 
+h = unit(0, "mm")
336 
+for(rot in seq(0, 360, by = 30)) {
311 337 
 	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = strrep(letters[1:10], 4), labels_rot = rot, which = "column", side = "bottom")
312 
-	pushViewport(viewport(layout.pos.col = 1, layout.pos.row = rot/30 + 1))
338 
+	h = h + height(anno)
339 
+	pushViewport(viewport(y = h, height = height(anno), just = "top"))
313 340 
 	grid.rect()
314 341 
 	draw(anno, index = 1:100)
315 342 
 	popViewport()
... ... 
@@ -317,10 +344,12 @@ for(rot in seq(0, 360, by = 30)[-13]) {
317 344
318 345
319 346 
 grid.newpage()
320 
-pushViewport(viewport(layout = grid.layout(nrow = 1, ncol = 12)))
321 
-for(rot in seq(0, 360, by = 30)[-13]) {
322 
-	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = strrep(letters[1:10], 4), labels_rot = rot, which = "row", side = "right")
323 
-	pushViewport(viewport(layout.pos.row = 1, layout.pos.col = rot/30 + 1))
347 
+pushViewport(viewport(w = 0.9, h = 0.9))
348 
+w = unit(0, "mm")
349 
+for(rot in seq(0, 360, by = 30)) {
350 
+	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = strrep(letters[1:10], 4), labels_rot = rot, which = "row", side = "left")
351 
+	w = w + width(anno)
352 
+	pushViewport(viewport(x = w, width = width(anno), just = "right"))
324 353 
 	grid.rect()
325 354 
 	draw(anno, index = 1:100)
326 355 
 	popViewport()
Browse code

update

Zuguang Gu authored on 19/10/2019 18:58:27
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @1dbbe82
... ... 
@@ -304,18 +304,28 @@ Heatmap(m) + rowAnnotation(mark = anno)
304 304 
 ht_list = Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)
305 305 
 draw(ht_list, row_split = c(rep("a", 95), rep("b", 5)))
306 306
307 
-pl = list()
307 
+
308 
+grid.newpage()
309 
+pushViewport(viewport(layout = grid.layout(nrow = 12, ncol = 1)))
308 310 
 for(rot in seq(0, 360, by = 30)[-13]) {
309 
-	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = letters[1:10], labels_rot = rot, which = "column")
310 
-	pl[[as.character(rot)]] = grid.grabExpr(draw(anno, index = 1:100, test = qq("labels_rot = @{rot}")))
311 
+	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = strrep(letters[1:10], 4), labels_rot = rot, which = "column", side = "bottom")
312 
+	pushViewport(viewport(layout.pos.col = 1, layout.pos.row = rot/30 + 1))
313 
+	grid.rect()
314 
+	draw(anno, index = 1:100)
315 
+	popViewport()
311 316 
 }
312 
-pushViewport(viewport(layout = grid.layout(nrow = 12, ncol = 1)))
313 
-for(i in seq_along(pl)) {
314 
-	pushViewport(viewport(layout.pos.row = i, layout.pos.col = 1))
315 
-	grid.draw(pl[[i]])
317 
+
318 
+
319 
+grid.newpage()
320 
+pushViewport(viewport(layout = grid.layout(nrow = 1, ncol = 12)))
321 
+for(rot in seq(0, 360, by = 30)[-13]) {
322 
+	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = strrep(letters[1:10], 4), labels_rot = rot, which = "row", side = "right")
323 
+	pushViewport(viewport(layout.pos.row = 1, layout.pos.col = rot/30 + 1))
324 
+	grid.rect()
325 
+	draw(anno, index = 1:100)
316 326 
 	popViewport()
317 327 
 }
318 
-popViewport()
328 
+
319 329
320 330
321 331 
 ### graphic parameters after reordering
Browse code

generate documentations by pkgdown

Zuguang Gu authored on 18/10/2019 11:34:02
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @1cb7fea
... ... 
@@ -304,6 +304,19 @@ Heatmap(m) + rowAnnotation(mark = anno)
304 304 
 ht_list = Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)
305 305 
 draw(ht_list, row_split = c(rep("a", 95), rep("b", 5)))
306 306
307 
+pl = list()
308 
+for(rot in seq(0, 360, by = 30)[-13]) {
309 
+	anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = letters[1:10], labels_rot = rot, which = "column")
310 
+	pl[[as.character(rot)]] = grid.grabExpr(draw(anno, index = 1:100, test = qq("labels_rot = @{rot}")))
311 
+}
312 
+pushViewport(viewport(layout = grid.layout(nrow = 12, ncol = 1)))
313 
+for(i in seq_along(pl)) {
314 
+	pushViewport(viewport(layout.pos.row = i, layout.pos.col = 1))
315 
+	grid.draw(pl[[i]])
316 
+	popViewport()
317 
+}
318 
+popViewport()
319 
+
307 320
308 321 
 ### graphic parameters after reordering
309 322 
 index = c(1, 3, 5, 7, 9, 2, 4, 6, 8, 10)
Browse code

support heatmap_legend_offset

Zuguang Gu authored on 05/07/2019 20:23:56
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @5841d84
... ... 
@@ -293,7 +293,7 @@ draw(anno, test = "heatmap, colors")
293 293 
 anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
294 294 
 draw(anno, index = 1:100, test = "anno_mark")
295 295
296 
-anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], labels_rot = 30, which = "row")
296 
+anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], labels_rot = 30, which = "column")
297 297 
 draw(anno, index = 1:100, test = "anno_mark")
298 298
299 299 
 m = matrix(1:1000, byrow = TRUE, nr = 100)
Browse code

add labels_rot argument to anno_mark()

Zuguang Gu authored on 02/07/2019 20:34:44
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @f4dac00
... ... 
@@ -293,8 +293,11 @@ draw(anno, test = "heatmap, colors")
293 293 
 anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
294 294 
 draw(anno, index = 1:100, test = "anno_mark")
295 295
296 
+anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], labels_rot = 30, which = "row")
297 
+draw(anno, index = 1:100, test = "anno_mark")
298 
+
296 299 
 m = matrix(1:1000, byrow = TRUE, nr = 100)
297 
-anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
300 
+anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row", labels_rot = 30)
298 301 
 Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)
299 302 
 Heatmap(m) + rowAnnotation(mark = anno)
300 303
Browse code

support reverse axes for annotations

Zuguang Gu authored on 18/04/2019 09:52:51
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @5ffb507
... ... 
@@ -123,6 +123,12 @@ anno = anno_points(c(1:5, NA, 7:10))
123 123 
 draw(anno, test = "anno_points")
124 124
125 125
126 
+anno = anno_points(runif(10), axis_param = list(direction = "reverse"), ylim = c(0, 1))
127 
+draw(anno, test = "anno_points")
128 
+
129 
+anno = anno_points(runif(10), axis_param = list(direction = "reverse"), ylim = c(0, 1), which = "row")
130 
+draw(anno, test = "anno_points")
131 
+
126 132 
 ##### test anno_lines ###
127 133 
 anno = anno_lines(runif(10))
128 134 
 draw(anno, test = "anno_lines")
... ... 
@@ -146,6 +152,8 @@ draw(anno, test = "anno_lines, smooth, matrix, by row")
146 152 
 anno = anno_lines(c(1:5, NA, 7:10))
147 153 
 draw(anno, test = "anno_lines")
148 154
155 
+anno = anno_lines(runif(10), axis_param = list(direction = "reverse"))
156 
+draw(anno, test = "anno_lines")
149 157
150 158 
 ###### test anno_text #######
151 159 
 anno = anno_text(month.name)
... ... 
@@ -199,6 +207,16 @@ draw(anno, test = "proportion matrix")
199 207 
 anno = anno_barplot(c(1:5, NA, 7:10))
200 208 
 draw(anno, test = "a vector")
201 209
210 
+anno = anno_barplot(1:10, which = "row", axis_param = list(direction = "reverse"))
211 
+draw(anno, test = "a vector")
212 
+
213 
+anno = anno_barplot(1:10, baseline = 5, which = "row", axis_param = list(direction = "reverse"))
214 
+draw(anno, test = "a vector")
215 
+
216 
+anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), which = "row", axis_param = list(direction = "reverse"))
217 
+draw(anno, test = "a vector")
218 
+
219 
+
202 220 
 ##### test anno_boxplot #####
203 221 
 set.seed(123)
204 222 
 m = matrix(rnorm(100), 10)
Browse code

add test script for the heatmap annotation size

jokergoo authored on 15/03/2019 13:47:43
Showing1 changed files
tests_not_run/test-AnnotationFunction.R
History View file @0c139e2
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,496 @@
1 
+
2 
+normalize_graphic_param_to_mat(1, nc = 2, nr = 4, "foo")
3 
+normalize_graphic_param_to_mat(1:2, nc = 2, nr = 4, "foo")
4 
+normalize_graphic_param_to_mat(1:4, nc = 2, nr = 4, "foo")
5 
+
6 
+### AnnotationFunction constructor #####
7 
+fun = function(index) {
8 
+	x = runif(10)
9 
+	pushViewport(viewport(xscale = c(0.5, 10.5), yscale = c(0, 1)))
10 
+	grid.points(index, x[index])
11 
+	popViewport()
12 
+}
13 
+anno = AnnotationFunction(fun = fun)
14 
+
15 
+x = runif(10)
16 
+fun = function(index) {
17 
+	pushViewport(viewport(xscale = c(0.5, 10.5), yscale = c(0, 1)))
18 
+	grid.points(index, x[index])
19 
+	popViewport()
20 
+}
21 
+anno = AnnotationFunction(fun = fun, var_imported = "x")
22 
+anno = AnnotationFunction(fun = fun, var_imported = list(x))
23 
+
24 
+
25 
+devAskNewPage(ask = TRUE)
26 
+
27 
+########### testing anno_simple ############
28 
+anno = anno_simple(1:10)
29 
+draw(anno, test = "as a simple vector")
30 
+draw(anno[1:5], test = "subset of column annotation")
31 
+anno = anno_simple(1:10, which = "row")
32 
+draw(anno, test = "as row annotation")
33 
+draw(anno[1:5], test = "subste of row annotation")
34 
+
35 
+anno = anno_simple(1:10, col = structure(rand_color(10), names = 1:10))
36 
+draw(anno, test = "self-define colors")
37 
+
38 
+anno = anno_simple(1:10, border = TRUE)
39 
+draw(anno, test = "border")
40 
+anno = anno_simple(1:10, gp = gpar(col = "red"))
41 
+draw(anno, test = "gp for the grids")
42 
+
43 
+anno = anno_simple(c(1:9, NA))
44 
+draw(anno, test = "vector has NA values")
45 
+
46 
+anno = anno_simple(cbind(1:10, 10:1))
47 
+draw(anno, test = "a matrix")
48 
+draw(anno[1:5], test = "subste of a matrix")
49 
+
50 
+anno = anno_simple(1:10, pch = 1, pt_gp = gpar(col = "red"), pt_size = unit(seq(1, 10), "mm"))
51 
+draw(anno, test = "with symbols + pt_gp + pt_size")
52 
+anno = anno_simple(1:10, pch = 1:10)
53 
+draw(anno, test = "pch is a vector")
54 
+anno = anno_simple(1:10, pch = c(1:4, NA, 6:8, NA, 10, 11))
55 
+draw(anno, test = "pch has NA values")
56 
+
57 
+anno = anno_simple(cbind(1:10, 10:1), pch = 1, pt_gp = gpar(col = "blue"))
58 
+draw(anno, test = "matrix with symbols")
59 
+anno = anno_simple(cbind(1:10, 10:1), pch = 1:2)
60 
+draw(anno, test = "matrix, length of pch is number of annotations")
61 
+anno = anno_simple(cbind(1:10, 10:1), pch = 1:10)
62 
+draw(anno, test = "matrix, length of pch is length of samples")
63 
+anno = anno_simple(cbind(1:10, 10:1), pch = matrix(1:20, nc = 2))
64 
+draw(anno, test = "matrix, pch is a matrix")
65 
+pch = matrix(1:20, nc = 2)
66 
+pch[sample(length(pch), 10)] = NA
67 
+anno = anno_simple(cbind(1:10, 10:1), pch = pch)
68 
+draw(anno, test = "matrix, pch is a matrix with NA values")
69 
+
70 
+
71 
+####### test anno_empty ######
72 
+anno = anno_empty()
73 
+draw(anno, test = "anno_empty")
74 
+anno = anno_empty(border = FALSE)
75 
+draw(anno, test = "anno_empty without border")
76 
+
77 
+###### test anno_image #####
78 
+image1 = sample(dir("~/Downloads/IcoMoon-Free-master/PNG/64px", full.names = TRUE), 10)
79 
+anno = anno_image(image1)
80 
+draw(anno, test = "png")
81 
+draw(anno[1:5], test = "subset of png")
82 
+anno = anno_image(image1, which = "row")
83 
+draw(anno, test = "png on rows")
84 
+image2 = sample(dir("~/Downloads/IcoMoon-Free-master/SVG/", full.names = TRUE), 10)
85 
+anno = anno_image(image2)
86 
+draw(anno, test = "svg")
87 
+image3 = sample(dir("~/Downloads/IcoMoon-Free-master/EPS/", full.names = TRUE), 10)
88 
+anno = anno_image(image3)
89 
+draw(anno, test = "eps")
90 
+image4 = sample(dir("~/Downloads/IcoMoon-Free-master/PDF/", full.names = TRUE), 10)
91 
+anno = anno_image(image4)
92 
+draw(anno, test = "pdf")
93 
+
94 
+anno = anno_image(c(image1[1:3], image2[1:3], image3[1:3], image4[1:3]))
95 
+draw(anno, test = "png+svg+eps+pdf")
96 
+
97 
+anno = anno_image(image1, gp = gpar(fill = 1:10, col = "black"))
98 
+draw(anno, test = "png + gp")
99 
+draw(anno[1:5], test = "png + gp")
100 
+
101 
+anno = anno_image(image1, space = unit(3, "mm"))
102 
+draw(anno, test = "space")
103 
+
104 
+image1[1] = ""
105 
+anno = anno_image(image1)
106 
+draw(anno, test = "png")
107 
+
108 
+######## test anno_points #####
109 
+anno = anno_points(runif(10))
110 
+draw(anno, test = "anno_points")
111 
+anno = anno_points(matrix(runif(20), nc = 2), pch = 1:2)
112 
+draw(anno, test = "matrix")
113 
+anno = anno_points(c(1:5, 1:5))
114 
+draw(anno, test = "anno_points")
115 
+anno = anno_points(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3))
116 
+draw(anno, test = "matrix")
117 
+
118 
+anno = anno_points(1:10, gp = gpar(col = rep(2:3, each = 5)), pch = rep(2:3, each = 5))
119 
+draw(anno, test = "anno_points")
120 
+draw(anno, index = c(1, 3, 5, 7, 9, 2, 4, 6, 8, 10), test = "anno_points")
121 
+
122 
+anno = anno_points(c(1:5, NA, 7:10))
123 
+draw(anno, test = "anno_points")
124 
+
125 
+
126 
+##### test anno_lines ###
127 
+anno = anno_lines(runif(10))
128 
+draw(anno, test = "anno_lines")
129 
+anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3))
130 
+draw(anno, test = "matrix")
131 
+anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3),
132 
+	add_points = TRUE, pt_gp = gpar(col = 5:6), pch = c(1, 16))
133 
+draw(anno, test = "matrix")
134 
+anno = anno_lines(sort(rnorm(10)), height = unit(2, "cm"), smooth = TRUE, add_points = TRUE)
135 
+draw(anno, test = "anno_lines, smooth")
136 
+anno = anno_lines(cbind(sort(rnorm(10)), sort(rnorm(10), decreasing = TRUE)),
137 
+	height = unit(2, "cm"), smooth = TRUE, add_points = TRUE, gp = gpar(col = 2:3))
138 
+draw(anno, test = "anno_lines, smooth, matrix")
139 
+
140 
+anno = anno_lines(sort(rnorm(10)), width = unit(2, "cm"), smooth = TRUE, add_points = TRUE, which = "row")
141 
+draw(anno, test = "anno_lines, smooth, by row")
142 
+anno = anno_lines(cbind(sort(rnorm(10)), sort(rnorm(10), decreasing = TRUE)),
143 
+	width = unit(2, "cm"), smooth = TRUE, add_points = TRUE, gp = gpar(col = 2:3), which = "row")
144 
+draw(anno, test = "anno_lines, smooth, matrix, by row")
145 
+
146 
+anno = anno_lines(c(1:5, NA, 7:10))
147 
+draw(anno, test = "anno_lines")
148 
+
149 
+
150 
+###### test anno_text #######
151 
+anno = anno_text(month.name)
152 
+draw(anno, test = "month names")
153 
+anno = anno_text(month.name, gp = gpar(fontsize = 16))
154 
+draw(anno, test = "month names with fontsize")
155 
+anno = anno_text(month.name, gp = gpar(fontsize = 1:12+4))
156 
+draw(anno, test = "month names with changing fontsize")
157 
+anno = anno_text(month.name, which = "row")
158 
+draw(anno, test = "month names on rows")
159 
+anno = anno_text(month.name, location = 0, rot = 45, just = "left", gp = gpar(col = 1:12))
160 
+draw(anno, test = "with rotations")
161 
+anno = anno_text(month.name, location = 1, rot = 45, just = "right", gp = gpar(fontsize = 1:12+4))
162 
+draw(anno, test = "with rotations")
163 
+
164 
+devAskNewPage(ask = TRUE)
165 
+for(rot in seq(0, 360, by = 45)) {
166 
+	anno = anno_text(month.name, which = "row", location = 0, rot = rot,
167 
+		just = "left")
168 
+	draw(anno, test = paste0("rot =", rot))
169 
+}
170 
+
171 
+
172 
+
173 
+##### test anno_barplot #####
174 
+anno = anno_barplot(1:10)
175 
+draw(anno, test = "a vector")
176 
+draw(anno[1:5], test = "a vector, subset")
177 
+anno = anno_barplot(1:10, which = "row")
178 
+draw(anno, test = "a vector")
179 
+anno = anno_barplot(1:10, bar_width = 1)
180 
+draw(anno, test = "bar_width")
181 
+anno = anno_barplot(1:10, gp = gpar(fill = 1:10))
182 
+draw(anno, test = "fill colors")
183 
+
184 
+anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)))
185 
+draw(anno, test = "a matrix")
186 
+draw(anno[1:5], test = "a matrix, subset")
187 
+anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), which = "row")
188 
+draw(anno, test = "a matrix, on rows")
189 
+anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), gp = gpar(fill = 2:3, col = 2:3))
190 
+draw(anno, test = "a matrix with fill")
191 
+
192 
+m = matrix(runif(4*10), nc = 4)
193 
+m = t(apply(m, 1, function(x) x/sum(x)))
194 
+anno = anno_barplot(m)
195 
+draw(anno, test = "proportion matrix")
196 
+anno = anno_barplot(m, gp = gpar(fill = 2:5), bar_width = 1, height = unit(6, "cm"))
197 
+draw(anno, test = "proportion matrix")
198 
+
199 
+anno = anno_barplot(c(1:5, NA, 7:10))
200 
+draw(anno, test = "a vector")
201 
+
202 
+##### test anno_boxplot #####
203 
+set.seed(123)
204 
+m = matrix(rnorm(100), 10)
205 
+anno = anno_boxplot(m, height = unit(4, "cm"))
206 
+draw(anno, test = "anno_boxplot")
207 
+draw(anno[1:5], test = "subset")
208 
+anno = anno_boxplot(m, height = unit(4, "cm"), gp = gpar(fill = 1:10))
209 
+draw(anno, test = "anno_boxplot with gp")
210 
+anno = anno_boxplot(m, height = unit(4, "cm"), box_width = 0.9)
211 
+draw(anno, test = "anno_boxplot with box_width")
212 
+
213 
+m = matrix(rnorm(100), 10)
214 
+m[1, ] = NA
215 
+anno = anno_boxplot(m, height = unit(4, "cm"))
216 
+draw(anno, test = "anno_boxplot")
217 
+
218 
+
219 
+####### test anno_joyplot ####
220 
+m = matrix(rnorm(1000), nc = 10)
221 
+lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")]))
222 
+anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row")
223 
+draw(anno, test = "joyplot")
224 
+anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", gp = gpar(fill = 1:10))
225 
+draw(anno, test = "joyplot + col")
226 
+anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", scale = 1)
227 
+draw(anno, test = "joyplot + scale")
228 
+
229 
+m = matrix(rnorm(5000), nc = 50)
230 
+lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")]))
231 
+anno = anno_joyplot(lt, width = unit(4, "cm"), which = "row", gp = gpar(fill = NA), scale = 4)
232 
+draw(anno, test = "joyplot")
233 
+
234 
+######## test anno_horizon ######
235 
+lt = lapply(1:20, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1)
236 
+anno = anno_horizon(lt, which = "row")
237 
+draw(anno, test = "horizon chart")
238 
+anno = anno_horizon(lt, which = "row", gp = gpar(pos_fill = "orange", neg_fill = "darkgreen"))
239 
+draw(anno, test = "horizon chart, col")
240 
+anno = anno_horizon(lt, which = "row", negative_from_top = TRUE)
241 
+draw(anno, test = "horizon chart + negative_from_top")
242 
+anno = anno_horizon(lt, which = "row", gap = unit(1, "mm"))
243 
+draw(anno, test = "horizon chart + gap")
244 
+anno = anno_horizon(lt, which = "row", gp = gpar(pos_fill = rep(c("orange", "red"), each = 10),
245 
+	neg_fill = rep(c("darkgreen", "blue"), each = 10)))
246 
+draw(anno, test = "horizon chart, col")
247 
+
248 
+####### test anno_histogram ####
249 
+m = matrix(rnorm(1000), nc = 10)
250 
+anno = anno_histogram(t(m), which = "row")
251 
+draw(anno, test = "row histogram")
252 
+draw(anno[1:5], test = "subset row histogram")
253 
+anno = anno_histogram(t(m), which = "row", gp = gpar(fill = 1:10))
254 
+draw(anno, test = "row histogram with color")
255 
+anno = anno_histogram(t(m), which = "row", n_breaks = 20)
256 
+draw(anno, test = "row histogram with color")
257 
+m[1, ] = NA
258 
+anno = anno_histogram(t(m), which = "row")
259 
+draw(anno, test = "row histogram")
260 
+
261 
+
262 
+####### test anno_density ######
263 
+anno = anno_density(t(m), which = "row")
264 
+draw(anno, test = "normal density")
265 
+draw(anno[1:5], test = "normal density, subset")
266 
+anno = anno_density(t(m), which = "row", type = "violin")
267 
+draw(anno, test = "violin")
268 
+anno = anno_density(t(m), which = "row", type = "heatmap")
269 
+draw(anno, test = "heatmap")
270 
+anno = anno_density(t(m), which = "row", type = "heatmap", heatmap_colors = c("white", "orange"))
271 
+draw(anno, test = "heatmap, colors")
272 
+
273 
+
274 
+###### anno_mark ###
275 
+anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
276 
+draw(anno, index = 1:100, test = "anno_mark")
277 
+
278 
+m = matrix(1:1000, byrow = TRUE, nr = 100)
279 
+anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
280 
+Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)
281 
+Heatmap(m) + rowAnnotation(mark = anno)
282 
+
283 
+ht_list = Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)
284 
+draw(ht_list, row_split = c(rep("a", 95), rep("b", 5)))
285 
+
286 
+
287 
+### graphic parameters after reordering
288 
+index = c(1, 3, 5, 7, 9, 2, 4, 6, 8, 10)
289 
+anno = anno_simple(1:10, pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
290 
+	pt_size = unit(1:10, "mm"))
291 
+draw(anno, index, test = "a numeric vector")
292 
+anno = anno_simple(1:10, pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
293 
+	pt_size = unit(1:10, "mm"), which = "row")
294 
+draw(anno, index, test = "a numeric vector")
295 
+
296 
+
297 
+anno = anno_points(1:10, pch = 1:10, gp = gpar(col = rep(c(1, 2), each = 5)),
298 
+	size = unit(1:10, "mm"))
299 
+draw(anno, index, test = "a numeric vector")
300 
+anno = anno_points(1:10, pch = 1:10, gp = gpar(col = rep(c(1, 2), each = 5)),
301 
+	size = unit(1:10, "mm"), which = "row")
302 
+draw(anno, index, test = "a numeric vector")
303 
+
304 
+
305 
+anno = anno_lines(sort(runif(10)), pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
306 
+	size = unit(1:10, "mm"), add_points = TRUE)
307 
+draw(anno, index, test = "a numeric vector")
308 
+anno = anno_lines(sort(runif(10)), pch = 1:10, pt_gp = gpar(col = rep(c(1, 2), each = 5)),
309 
+	size = unit(1:10, "mm"), add_points = TRUE, which = "row")
310 
+draw(anno, index, test = "a numeric vector")
311 
+
312 
+
313 
+anno = anno_barplot(1:10, gp = gpar(fill = rep(c(1, 2), each = 5)))
314 
+draw(anno, index, test = "a numeric vector")
315 
+anno = anno_barplot(1:10, gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
316 
+draw(anno, index, test = "a numeric vector")
317 
+
318 
+anno = anno_barplot(cbind(1:10, 10:1), gp = gpar(fill = 1:2))
319 
+draw(anno, index, test = "a numeric vector")
320 
+anno = anno_barplot(cbind(1:10, 10:1), gp = gpar(fill = 1:2), which = "row")
321 
+draw(anno, index, test = "a numeric vector")
322 
+
323 
+
324 
+m = matrix(rnorm(100), 10)
325 
+m = m[, order(apply(m, 2, median))]
326 
+anno = anno_boxplot(m, pch = 1:10, gp = gpar(fill = rep(c(1, 2), each = 5)),
327 
+	size = unit(1:10, "mm"), height = unit(4, "cm"))
328 
+draw(anno, index, test = "a numeric vector")
329 
+anno = anno_boxplot(t(m), pch = 1:10, gp = gpar(fill = rep(c(1, 2), each = 5)),
330 
+	size = unit(1:10, "mm"), which = "row", width = unit(4, "cm"))
331 
+draw(anno, index, test = "a numeric vector")
332 
+
333 
+anno = anno_histogram(m, gp = gpar(fill = rep(c(1, 2), each = 5)))
334 
+draw(anno, index, test = "a numeric vector")
335 
+anno = anno_histogram(t(m), gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
336 
+draw(anno, index, test = "a numeric vector")
337 
+
338 
+anno = anno_density(m, gp = gpar(fill = rep(c(1, 2), each = 5)))
339 
+draw(anno, index, test = "a numeric vector")
340 
+anno = anno_density(t(m), gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
341 
+draw(anno, index, test = "a numeric vector")
342 
+
343 
+
344 
+anno = anno_density(m, type = "violin", gp = gpar(fill = rep(c(1, 2), each = 5)))
345 
+draw(anno, index, test = "a numeric vector")
346 
+anno = anno_density(t(m), type = "violin", gp = gpar(fill = rep(c(1, 2), each = 5)), which = "row")
347 
+draw(anno, index, test = "a numeric vector")
348 
+
349 
+
350 
+anno = anno_text(month.name, gp = gpar(col = rep(c(1, 2), each = 5)))
351 
+draw(anno, index, test = "a numeric vector")
352 
+anno = anno_text(month.name, gp = gpar(col = rep(c(1, 2), each = 5)), which= "row")
353 
+draw(anno, index, test = "a numeric vector")
354 
+
355 
+lt = lapply(1:10, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1)
356 
+anno = anno_horizon(lt, gp = gpar(pos_fill = rep(c(1, 2), each = 5), neg_fill = rep(c(3, 4), each = 5)), which = "row")
357 
+draw(anno, index, test = "a numeric vector")
358 
+
359 
+m = matrix(rnorm(1000), nc = 10)
360 
+lt = apply(m, 2, function(x) data.frame(density(x)[c("x", "y")]))
361 
+anno = anno_joyplot(lt, gp = gpar(fill = rep(c(1, 2), each = 5)),
362 
+	width = unit(4, "cm"), which = "row")
363 
+draw(anno, index, test = "joyplot")
364 
+
365 
+
366 
+anno = anno_block(gp = gpar(fill = 1:4))
367 
+draw(anno, index = 1:10, k = 1, n = 4, test = "anno_block")
368 
+draw(anno, index = 1:10, k = 2, n = 4, test = "anno_block")
369 
+
370 
+anno = anno_block(gp = gpar(fill = 1:4), labels = letters[1:4], labels_gp = gpar(col = "white"))
371 
+draw(anno, index = 1:10, k = 2, n = 4, test = "anno_block")
372 
+draw(anno, index = 1:10, k = 4, n = 4, test = "anno_block")
373 
+draw(anno, index = 1:10, k = 2, n = 2, test = "anno_block")
374 
+
375 
+anno = anno_block(gp = gpar(fill = 1:4), labels = letters[1:4], labels_gp = gpar(col = "white"), which = "row")
376 
+draw(anno, index = 1:10, k = 2, n = 4, test = "anno_block")
377 
+
378 
+
379 
+### anno_zoom
380 
+fa = sort(sample(letters[1:3], 100, replace = TRUE, prob = c(1, 2, 3)))
381 
+panel_fun = function(index, nm) {
382 
+	grid.rect()
383 
+	grid.text(nm)
384 
+}
385 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun)
386 
+draw(anno, index = 1:100, test = "anno_zoom")
387 
+
388 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
389 
+	gap = unit(1, "cm"))
390 
+draw(anno, index = 1:100, test = "anno_zoom, set gap")
391 
+
392 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
393 
+	size = 1:3)
394 
+draw(anno, index = 1:100, test = "anno_zoom, size set as relative values")
395 
+
396 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
397 
+	size = 1:3, extend = unit(1, "cm"))
398 
+draw(anno, index = 1:100, test = "anno_zoom, extend")
399 
+
400 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
401 
+	size = unit(1:3, "cm"))
402 
+draw(anno, index = 1:100, test = "anno_zoom, size set as absolute values")
403 
+
404 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
405 
+	size = unit(c(2, 20, 40), "cm"))
406 
+draw(anno, index = 1:100, test = "anno_zoom, big size")
407 
+
408 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
409 
+	size = 1:3, gap = unit(1, "cm"))
410 
+draw(anno, index = 1:100, test = "anno_zoom, size set as relative values, gap")
411 
+
412 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
413 
+	size = unit(1:3, "cm"), gap = unit(1, "cm"))
414 
+draw(anno, index = 1:100, test = "anno_zoom, size set as absolute values, gap")
415 
+
416 
+
417 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
418 
+	size = unit(1:3, "cm"), side = "left")
419 
+draw(anno, index = 1:100, test = "anno_zoom, side")
420 
+
421 
+
422 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
423 
+	size = unit(1:3, "cm"), link_gp = gpar(fill = 1:3))
424 
+draw(anno, index = 1:100, test = "anno_zoom, link_gp")
425 
+
426 
+anno = anno_zoom(align_to = fa, which = "row", panel_fun = panel_fun,
427 
+	size = unit(1:3, "cm"), link_gp = gpar(fill = 1:3),
428 
+	link_width = unit(2, "cm"), width = unit(4, "cm"))
429 
+draw(anno, index = 1:100, test = "anno_zoom, width")
430 
+
431 
+anno = anno_zoom(align_to = list(a = 1:10, b = 30:45, c = 70:90),
432 
+	which = "row", panel_fun = panel_fun, size = unit(1:3, "cm"))
433 
+draw(anno, index = 1:100, test = "anno_zoom, a list of indices")
434 
+
435 
+anno = anno_zoom(align_to = fa, which = "column", panel_fun = panel_fun,
436 
+	size = unit(1:3, "cm"))
437 
+draw(anno, index = 1:100, test = "anno_zoom, column annotation")
438 
+
439 
+
440 
+m = matrix(rnorm(100*10), nrow = 100)
441 
+hc = hclust(dist(m))
442 
+fa2 = cutree(hc, k = 4)
443 
+anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun)
444 
+draw(anno, index = hc$order, test = "anno_zoom, column annotation")
445 
+
446 
+anno = anno_zoom(align_to = fa2, which = "column", panel_fun = panel_fun)
447 
+draw(anno, index = hc$order, test = "anno_zoom, column annotation")
448 
+
449 
+
450 
+anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun)
451 
+Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno))
452 
+Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno), row_split = 2)
453 
+
454 
+
455 
+anno = anno_zoom(align_to = fa2, which = "row", panel_fun = panel_fun, size = unit(1:4, "cm"))
456 
+Heatmap(m, cluster_rows = hc, right_annotation = rowAnnotation(foo = anno))
457 
+
458 
+set.seed(123)
459 
+m = matrix(rnorm(100*10), nrow = 100)
460 
+subgroup = sample(letters[1:3], 100, replace = TRUE, prob = c(1, 5, 10))
461 
+rg = range(m)
462 
+panel_fun = function(index, nm) {
463 
+	pushViewport(viewport(xscale = rg, yscale = c(0, 2)))
464 
+	grid.rect()
465 
+	grid.xaxis(gp = gpar(fontsize = 8))
466 
+	grid.boxplot(m[index, ], pos = 1, direction = "horizontal")
467 
+	grid.text(paste("distribution of group", nm), mean(rg), y = 1.9,
468 
+		just = "top", default.units = "native", gp = gpar(fontsize = 10))
469 
+	popViewport()
470 
+}
471 
+anno = anno_zoom(align_to = subgroup, which = "row", panel_fun = panel_fun,
472 
+	size = unit(2, "cm"), gap = unit(1, "cm"), width = unit(4, "cm"))
473 
+Heatmap(m, right_annotation = rowAnnotation(foo = anno), row_split = subgroup)
474 
+
475 
+panel_fun2 = function(index, nm) {
476 
+	pushViewport(viewport())
477 
+	grid.rect()
478 
+	n = floor(length(index)/4)
479 
+	txt = paste("gene function", 1:n, collapse = "\n")
480 
+	grid.text(txt, 0.95, 0.5, default.units = "npc", just = "right", gp = gpar(fontsize = 8))
481 
+	popViewport()
482 
+}
483 
+anno2 = anno_zoom(align_to = subgroup, which = "row", panel_fun = panel_fun2,
484 
+	gap = unit(1, "cm"), width = unit(3, "cm"), side = "left")
485 
+
486 
+# in infinite loop
487 
+Heatmap(m, right_annotation = rowAnnotation(subgroup = subgroup, foo = anno,
488 
+	show_annotation_name = FALSE),
489 
+	left_annotation = rowAnnotation(bar = anno2, subgroup = subgroup, show_annotation_name = FALSE),
490 
+	show_row_dend = FALSE,
491 
+	row_split = subgroup)
492 
+
493 
+Heatmap(m, right_annotation = rowAnnotation(foo = anno),
494 
+	left_annotation = rowAnnotation(bar = anno2),
495 
+	show_row_dend = FALSE,
496 
+	row_split = subgroup)