1. ComplexHeatmap
  2. tests_not_run
  3. test-HeatmapList-class.R
Browse code

add unit_to_numeric() function

jokergoo authored on 05/03/2020 14:31:53
Showing 1 changed files
tests_not_run/test-HeatmapList-class.R
History View file @ d574e5ea
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-
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-ht_global_opt$verbose = FALSE
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-ht_global_opt$show_vp_border = FALSE
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-
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-set.seed(123)
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-nr1 = 10; nr2 = 8; nr3 = 6
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-nc1 = 6; nc2 = 8; nc3 = 10
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-mat1 = cbind(rbind(matrix(rnorm(nr1*nc1, mean = 1,   sd = 0.5), nr = nr1),
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-          matrix(rnorm(nr2*nc1, mean = 0,   sd = 0.5), nr = nr2),
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-          matrix(rnorm(nr3*nc1, mean = 0,   sd = 0.5), nr = nr3)),
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-    rbind(matrix(rnorm(nr1*nc2, mean = 0,   sd = 0.5), nr = nr1),
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-          matrix(rnorm(nr2*nc2, mean = 1,   sd = 0.5), nr = nr2),
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-          matrix(rnorm(nr3*nc2, mean = 0,   sd = 0.5), nr = nr3)),
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-    rbind(matrix(rnorm(nr1*nc3, mean = 0.5, sd = 0.5), nr = nr1),
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-          matrix(rnorm(nr2*nc3, mean = 0.5, sd = 0.5), nr = nr2),
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-          matrix(rnorm(nr3*nc3, mean = 1,   sd = 0.5), nr = nr3))
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-   )
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-
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-rownames(mat1) = paste0("row_1_", seq_len(nrow(mat1)))
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-colnames(mat1) = paste0("column_1_", seq_len(nrow(mat1)))
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-
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-nr3 = 10; nr1 = 8; nr2 = 6
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-nc3 = 6; nc1 = 8; nc2 = 10
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-mat2 = cbind(rbind(matrix(rnorm(nr1*nc1, mean = 1,   sd = 0.5), nr = nr1),
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-          matrix(rnorm(nr2*nc1, mean = 0,   sd = 0.5), nr = nr2),
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-          matrix(rnorm(nr3*nc1, mean = 0,   sd = 0.5), nr = nr3)),
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-    rbind(matrix(rnorm(nr1*nc2, mean = 0,   sd = 0.5), nr = nr1),
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-          matrix(rnorm(nr2*nc2, mean = 1,   sd = 0.5), nr = nr2),
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-          matrix(rnorm(nr3*nc2, mean = 0,   sd = 0.5), nr = nr3)),
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-    rbind(matrix(rnorm(nr1*nc3, mean = 0.5, sd = 0.5), nr = nr1),
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-          matrix(rnorm(nr2*nc3, mean = 0.5, sd = 0.5), nr = nr2),
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-          matrix(rnorm(nr3*nc3, mean = 1,   sd = 0.5), nr = nr3))
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-   )
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-
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-rownames(mat2) = paste0("row_2_", seq_len(nrow(mat2)))
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-colnames(mat2) = paste0("column_2_", seq_len(nrow(mat2)))
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-
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-
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-ht_list = Heatmap(mat1) + Heatmap(mat2)
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-ht_list
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-
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-######### legend ############
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-draw(ht_list, heatmap_legend_side = "bottom")
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-draw(ht_list, heatmap_legend_side = "left")
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-draw(ht_list, heatmap_legend_side = "top")
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-
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-
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-########## width #############
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-Heatmap(mat1, width = unit(6, "cm")) + Heatmap(mat2)
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-Heatmap(mat1) + Heatmap(mat2, width = unit(8, "cm"))
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-Heatmap(mat1, width = unit(12, "cm")) + Heatmap(mat2, width = unit(8, "cm"))
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-
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-Heatmap(mat1, heatmap_body_width = unit(6, "cm")) + Heatmap(mat2)
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-Heatmap(mat1) + Heatmap(mat2, heatmap_body_width = unit(6, "cm"))
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-Heatmap(mat1, heatmap_body_width = unit(6, "cm")) + Heatmap(mat2, heatmap_body_width = unit(6, "cm"))
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-Heatmap(mat1, heatmap_body_width = 4) + Heatmap(mat2)
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-
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-Heatmap(mat1, heatmap_body_width = 2) + Heatmap(mat2, heatmap_body_width = 1)
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-
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-
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-########### height ###########
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-Heatmap(mat1, height = unit(6, "cm")) + Heatmap(mat2)
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-Heatmap(mat1, heatmap_body_height = unit(6, "cm")) + Heatmap(mat2)
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-ht_list = Heatmap(mat1, heatmap_body_width = unit(6, "cm"), height = unit(6, "cm")) +
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-	Heatmap(mat2, heatmap_body_width = unit(6, "cm"), height = unit(6, "cm"))
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-draw(ht_list, column_title = "foooooooooo", row_title = "baaaaaaaaaaar")
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-
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-##### split #####
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-ht_list = Heatmap(mat1, name = "m1", row_km = 2) + Heatmap(mat2, name = "m2", row_km = 3)
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-draw(ht_list, main_heatmap = "m1")
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-draw(ht_list, main_heatmap = "m2")
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-
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-ht_list = Heatmap(mat1, name = "m1", row_km = 2, column_km = 3, width = unit(8, "cm"), height = unit(6, "cm")) +
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-	Heatmap(mat2, name = "m2", row_km = 3, column_km = 2, width = unit(8, "cm"), height = unit(10, "cm"))
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-draw(ht_list, main_heatmap = "m1", column_title = "foooooooooo", row_title = "baaaaaaaaaaar")
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-draw(ht_list, main_heatmap = "m2", column_title = "foooooooooo", row_title = "baaaaaaaaaaar")
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-
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-##### adjust column annotations #####
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-ha1 = HeatmapAnnotation(foo = 1:24, bar = anno_points(24:1, height = unit(4, "cm")))
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-ha2 = HeatmapAnnotation(bar = anno_points(24:1), foo = 1:24)
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-Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2, top_annotation = ha2)
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-ha2 = HeatmapAnnotation(foo = 1:24)
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-Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2, top_annotation = ha2)
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-Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2)
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-Heatmap(mat1, bottom_annotation = ha1) + Heatmap(mat2)
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-
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-
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-#### row annotations #####
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-ha = rowAnnotation(foo = 1:24, bar = anno_points(24:1), width = unit(6, "cm"))
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-Heatmap(mat1) + ha
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-Heatmap(mat1, width = unit(6, "cm")) + ha
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-Heatmap(mat1, width = unit(6, "cm"), row_km = 2) + ha
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-
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-
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-ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") +
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-  rowAnnotation(foo = 1:10, bar = anno_points(10:1)) +
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-  Heatmap(matrix(runif(100), 10), name = "runif")
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-summary(ht_list[1:5, ])
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-summary(ht_list[1:5, 1])
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-summary(ht_list[1:5, "rnorm"])
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-summary(ht_list[1:5, c("rnorm", "foo")])
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-
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-ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") %v%
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-  columnAnnotation(foo = 1:10, bar = anno_points(10:1)) %v%
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-  Heatmap(matrix(runif(100), 10), name = "runif")
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-summary(ht_list[, 1:5])
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-summary(ht_list[1, 1:5])
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-summary(ht_list["rnorm", 1:5])
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-summary(ht_list[c("rnorm", "foo"), 1:5])
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-
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-
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-
Browse code

add test script for the heatmap annotation size

jokergoo authored on 15/03/2019 13:47:43
Showing 1 changed files
tests_not_run/test-HeatmapList-class.R
History View file @ 0c139e20
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+
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+ht_global_opt$verbose = FALSE
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+ht_global_opt$show_vp_border = FALSE
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+
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+set.seed(123)
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+nr1 = 10; nr2 = 8; nr3 = 6
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+nc1 = 6; nc2 = 8; nc3 = 10
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+mat1 = cbind(rbind(matrix(rnorm(nr1*nc1, mean = 1,   sd = 0.5), nr = nr1),
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+          matrix(rnorm(nr2*nc1, mean = 0,   sd = 0.5), nr = nr2),
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+          matrix(rnorm(nr3*nc1, mean = 0,   sd = 0.5), nr = nr3)),
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+    rbind(matrix(rnorm(nr1*nc2, mean = 0,   sd = 0.5), nr = nr1),
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+          matrix(rnorm(nr2*nc2, mean = 1,   sd = 0.5), nr = nr2),
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+          matrix(rnorm(nr3*nc2, mean = 0,   sd = 0.5), nr = nr3)),
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+    rbind(matrix(rnorm(nr1*nc3, mean = 0.5, sd = 0.5), nr = nr1),
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+          matrix(rnorm(nr2*nc3, mean = 0.5, sd = 0.5), nr = nr2),
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+          matrix(rnorm(nr3*nc3, mean = 1,   sd = 0.5), nr = nr3))
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+   )
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+
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+rownames(mat1) = paste0("row_1_", seq_len(nrow(mat1)))
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+colnames(mat1) = paste0("column_1_", seq_len(nrow(mat1)))
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+
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+nr3 = 10; nr1 = 8; nr2 = 6
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+nc3 = 6; nc1 = 8; nc2 = 10
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+mat2 = cbind(rbind(matrix(rnorm(nr1*nc1, mean = 1,   sd = 0.5), nr = nr1),
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+          matrix(rnorm(nr2*nc1, mean = 0,   sd = 0.5), nr = nr2),
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+          matrix(rnorm(nr3*nc1, mean = 0,   sd = 0.5), nr = nr3)),
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+    rbind(matrix(rnorm(nr1*nc2, mean = 0,   sd = 0.5), nr = nr1),
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+          matrix(rnorm(nr2*nc2, mean = 1,   sd = 0.5), nr = nr2),
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+          matrix(rnorm(nr3*nc2, mean = 0,   sd = 0.5), nr = nr3)),
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+    rbind(matrix(rnorm(nr1*nc3, mean = 0.5, sd = 0.5), nr = nr1),
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+          matrix(rnorm(nr2*nc3, mean = 0.5, sd = 0.5), nr = nr2),
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+          matrix(rnorm(nr3*nc3, mean = 1,   sd = 0.5), nr = nr3))
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+   )
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+
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+rownames(mat2) = paste0("row_2_", seq_len(nrow(mat2)))
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+colnames(mat2) = paste0("column_2_", seq_len(nrow(mat2)))
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+
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+
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+ht_list = Heatmap(mat1) + Heatmap(mat2)
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+ht_list
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+
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+######### legend ############
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+draw(ht_list, heatmap_legend_side = "bottom")
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+draw(ht_list, heatmap_legend_side = "left")
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+draw(ht_list, heatmap_legend_side = "top")
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+
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+
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+########## width #############
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+Heatmap(mat1, width = unit(6, "cm")) + Heatmap(mat2)
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+Heatmap(mat1) + Heatmap(mat2, width = unit(8, "cm"))
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+Heatmap(mat1, width = unit(12, "cm")) + Heatmap(mat2, width = unit(8, "cm"))
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+
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+Heatmap(mat1, heatmap_body_width = unit(6, "cm")) + Heatmap(mat2)
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+Heatmap(mat1) + Heatmap(mat2, heatmap_body_width = unit(6, "cm"))
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+Heatmap(mat1, heatmap_body_width = unit(6, "cm")) + Heatmap(mat2, heatmap_body_width = unit(6, "cm"))
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+Heatmap(mat1, heatmap_body_width = 4) + Heatmap(mat2)
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+
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+Heatmap(mat1, heatmap_body_width = 2) + Heatmap(mat2, heatmap_body_width = 1)
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+
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+
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+########### height ###########
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+Heatmap(mat1, height = unit(6, "cm")) + Heatmap(mat2)
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+Heatmap(mat1, heatmap_body_height = unit(6, "cm")) + Heatmap(mat2)
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+ht_list = Heatmap(mat1, heatmap_body_width = unit(6, "cm"), height = unit(6, "cm")) +
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+	Heatmap(mat2, heatmap_body_width = unit(6, "cm"), height = unit(6, "cm"))
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+draw(ht_list, column_title = "foooooooooo", row_title = "baaaaaaaaaaar")
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+
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+##### split #####
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+ht_list = Heatmap(mat1, name = "m1", row_km = 2) + Heatmap(mat2, name = "m2", row_km = 3)
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+draw(ht_list, main_heatmap = "m1")
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+draw(ht_list, main_heatmap = "m2")
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+
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+ht_list = Heatmap(mat1, name = "m1", row_km = 2, column_km = 3, width = unit(8, "cm"), height = unit(6, "cm")) +
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+	Heatmap(mat2, name = "m2", row_km = 3, column_km = 2, width = unit(8, "cm"), height = unit(10, "cm"))
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+draw(ht_list, main_heatmap = "m1", column_title = "foooooooooo", row_title = "baaaaaaaaaaar")
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+draw(ht_list, main_heatmap = "m2", column_title = "foooooooooo", row_title = "baaaaaaaaaaar")
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+
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+##### adjust column annotations #####
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+ha1 = HeatmapAnnotation(foo = 1:24, bar = anno_points(24:1, height = unit(4, "cm")))
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+ha2 = HeatmapAnnotation(bar = anno_points(24:1), foo = 1:24)
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+Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2, top_annotation = ha2)
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+ha2 = HeatmapAnnotation(foo = 1:24)
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+Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2, top_annotation = ha2)
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+Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2)
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+Heatmap(mat1, bottom_annotation = ha1) + Heatmap(mat2)
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+
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+
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+#### row annotations #####
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+ha = rowAnnotation(foo = 1:24, bar = anno_points(24:1), width = unit(6, "cm"))
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+Heatmap(mat1) + ha
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+Heatmap(mat1, width = unit(6, "cm")) + ha
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+Heatmap(mat1, width = unit(6, "cm"), row_km = 2) + ha
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+
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+
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+ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") +
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+  rowAnnotation(foo = 1:10, bar = anno_points(10:1)) +
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+  Heatmap(matrix(runif(100), 10), name = "runif")
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+summary(ht_list[1:5, ])
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+summary(ht_list[1:5, 1])
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+summary(ht_list[1:5, "rnorm"])
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+summary(ht_list[1:5, c("rnorm", "foo")])
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+
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+ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") %v%
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+  columnAnnotation(foo = 1:10, bar = anno_points(10:1)) %v%
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+  Heatmap(matrix(runif(100), 10), name = "runif")
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+summary(ht_list[, 1:5])
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+summary(ht_list[1, 1:5])
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+summary(ht_list["rnorm", 1:5])
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+summary(ht_list[c("rnorm", "foo"), 1:5])
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+
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+
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+