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update

Zuguang Gu authored on 29/04/2019 07:51:08
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@@ -2,7 +2,7 @@ Package: ComplexHeatmap
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 Type: Package
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 Title: Make Complex Heatmaps
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 Version: 1.99.8
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-Date: 2019-04-25
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+Date: 2019-04-28
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 Author: Zuguang Gu
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 Maintainer: Zuguang Gu <z.gu@dkfz.de>
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 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices
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@@ -3,6 +3,9 @@ CHANGES in VERSION 1.99.8
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 * add `title_gap` in `Legend()
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 * fixed a bug of wrong row title spaces when multiple heatmaps are vertically
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   concatenated.
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+* fixed a bug of *_sub_title_side when the heatmap annotation is the first/last
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+  element in the heatmap list.
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+* zero-column/row heatmap is supported.
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 ========================
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@@ -358,14 +358,15 @@ Heatmap = function(matrix, col, name,
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     #     show_heatmap_legend = FALSE
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     #     .Object@heatmap_param$show_heatmap_legend = FALSE
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     # }
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-    if(ncol(matrix) == 0 && (!is.null(left_annotation) || !is.null(right_annotation))) {
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-        message_wrap("If you have row annotations for a zeor-column matrix, please directly use in form of `rowAnnotation(...) + NULL`")
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-        return(invisible(NULL))
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-    }
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-    if(nrow(matrix) == 0 && (!is.null(top_annotation) || !is.null(bottom_annotation))) {
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-        message_wrap("If you have column annotations for a zero-row matrix, please directly use in form of `HeatmapAnnotation(...) %v% NULL`")
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-        return(invisible(NULL))
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-    }
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+    
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+    # if(ncol(matrix) == 0 && (!is.null(left_annotation) || !is.null(right_annotation))) {
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+    #     message_wrap("If you have row annotations for a zeor-column matrix, please directly use in form of `rowAnnotation(...) + NULL`")
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+    #     return(invisible(NULL))
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+    # }
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+    # if(nrow(matrix) == 0 && (!is.null(top_annotation) || !is.null(bottom_annotation))) {
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+    #     message_wrap("If you have column annotations for a zero-row matrix, please directly use in form of `HeatmapAnnotation(...) %v% NULL`")
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+    #     return(invisible(NULL))
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+    # }
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     ### normalize km/split and row_km/row_split
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     if(missing(row_km)) row_km = km
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@@ -803,7 +804,7 @@ Heatmap = function(matrix, col, name,
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             row_anno_right_width = unit(0, "mm")
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         ),
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-        layout_index = NULL,
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+        layout_index = matrix(nrow = 0, ncol = 2),
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         graphic_fun_list = list(),
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         initialized = FALSE
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     )
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@@ -1488,7 +1489,8 @@ setMethod(f = "draw",
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         upViewport()
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     } else {
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         if(internal) {  # a heatmap without legend
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-            if(ncol(object@matrix) == 0 || nrow(object@matrix) == 0) return(invisible(NULL))
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+            # if(ncol(object@matrix) == 0 || nrow(object@matrix) == 0) return(invisible(NULL))
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+            if(nrow(object@layout$layout_index) == 0) return(invisible(NULL))
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             layout = grid.layout(nrow = length(HEATMAP_LAYOUT_COLUMN_COMPONENT), 
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                 ncol = length(HEATMAP_LAYOUT_ROW_COMPONENT), widths = component_width(object), 
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                 heights = component_height(object))
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@@ -1507,9 +1509,9 @@ setMethod(f = "draw",
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             }
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             upViewport()
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         } else {
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-            if(ncol(object@matrix) == 0) {
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-                stop_wrap("Single heatmap should contains a matrix with at least one column. Zero-column matrix can only be appended to the heatmap list.")
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-            }
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+            # if(ncol(object@matrix) == 0) {
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+            #     stop_wrap("Single heatmap should contains a matrix with at least one column. Zero-column matrix can only be appended to the heatmap list.")
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+            # }
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             ht_list = new("HeatmapList")
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             ht_list = add_heatmap(ht_list, object)
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             draw(ht_list, ...)
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@@ -524,9 +524,9 @@ setMethod(f = "make_layout",
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                 object@ht_list = c(list(Heatmap(matrix(nrow = nr, ncol = 0))), object@ht_list)
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                 ht_gap = unit.c(unit(0, "mm"), ht_gap)
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                 i_main = i_main + 1
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+                n_ht = n_ht + 1
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                 if(verbose) qqcat("add a zero-column heatmap for row dend/title on the very left\n")
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-            }
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-                
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+            }     
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         }
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         if(row_dend_side == "right" || row_sub_title_side == "right") {
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@@ -534,6 +534,7 @@ setMethod(f = "make_layout",
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             if(inherits(object@ht_list[[ length(object@ht_list) ]], "HeatmapAnnotation")) {
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                 object@ht_list = c(object@ht_list, list(Heatmap(matrix(nrow = nr, ncol = 0))))
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                 ht_gap = unit.c(ht_gap, unit(0, "mm"))
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+                n_ht = n_ht + 1
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                 if(verbose) qqcat("add a zero-column heatmap for row dend/title on the very right\n")
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             }
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         }
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@@ -546,6 +547,7 @@ setMethod(f = "make_layout",
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                 object@ht_list = c(list(Heatmap(matrix(nrow = 0, ncol = nc))), object@ht_list)
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                 ht_gap = unit.c(unit(0, "mm"), ht_gap)
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                 i_main = i_main + 1
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+                n_ht = n_ht + 1
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                 if(verbose) qqcat("add a zero-row heatmap for column dend/title on the very top\n")
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             }   
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         }
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@@ -554,6 +556,7 @@ setMethod(f = "make_layout",
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             if(inherits(object@ht_list[[ length(object@ht_list) ]], "HeatmapAnnotation")) {
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                 object@ht_list = c(object@ht_list, list(Heatmap(matrix(nrow = 0, ncol = nc))))
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                 ht_gap = unit.c(ht_gap, unit(0, "mm"))
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+                n_ht = n_ht + 1
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                 if(verbose) qqcat("add a zero-column heatmap for row dend/title on the very bottom\n")
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             }
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         }
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@@ -167,6 +167,20 @@ different results for different runs. To solve this problem, you do either way a
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    final consensus k-means clustering. Note you might still get different
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    results, but the chance is much smaller than just running k-means once.
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+### I only want to draw dendrograms plus a list of annotations.
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+
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+You need to assign the dendrograms to a zero-row/column matrix:
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+
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+```{r}
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+hc = hclust(dist(matrix(rnorm(100), 10)))
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+Heatmap(matrix(nc = 0, nr = 10), cluster_rows = hc, 
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+	right_annotation = rowAnnotation(
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+		foo = anno_points(1:10),
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+		sth = 1:10,
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+		bar = anno_barplot(1:10)),
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+	row_split = 2)
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+```
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+
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 ### I still have a problem with the package and I am lost in the ocean of the huge vignette.
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 The vignette (https://jokergoo.github.io/ComplexHeatmap-reference/book/)