Using heatmap in a panel of figures

[ghs101]

Hi,

I made a heatmap with Complexheatmap package I added a few filled rectangles+text with grid.rect and grid.text. I would like to grob this plot or save it as a gtable so I can add it to a panel. However I cant grob it or save it as a gtable object. I can only

library(ComplexHeatmap)

      set.seed(123)
      
      mat2 = matrix(rnorm(50*50), nrow = 50)
      
      ha = HeatmapAnnotation(
        empty = anno_empty(border = FALSE),
        foo = anno_block(gp = gpar(fill = 2:6), labels = LETTERS[1:5]))
      
      split = rep(1:5, each = 10)
      
     ht_list= Heatmap(mat2, name = "mat2", column_split = split, top_annotation = ha, 
              column_title = NULL)
      
      seekViewport("annotation_empty_1")
      loc1 = deviceLoc(x = unit(0, "npc"), y = unit(0, "npc"))
      seekViewport("annotation_empty_3")
      loc2 = deviceLoc(x = unit(1, "npc"), y = unit(1, "npc"))
      
      seekViewport("global")
      grid.rect(loc1$x, loc1$y, width = loc2$x - loc1$x, height = loc2$y - loc1$y, 
                just = c("left", "bottom"), gp = gpar(fill = "red"))
      grid.text("group 1", x = (loc1$x + loc2$x)*0.5, y = (loc1$y + loc2$y)*0.5)

gb_heatmap = grid.grabExpr(draw(ht_list, heatmap_legend_side = "right"))

hm_gtable <- gtable_matrix("hm_gtbl", matrix(list(gb_heatmap)), unit(1, "null"), unit(1, "null"))

when running thise code I the grid.rect and grid.text elements are not saved in the gtable object.

Help would be appreciated.

cheers,

[jokergoo]

You just put everything is a function and call grid.grabExpr() on that function:

make_plot = function() {
  set.seed(123)
      
      mat2 = matrix(rnorm(50*50), nrow = 50)
      
      ha = HeatmapAnnotation(
        empty = anno_empty(border = FALSE),
        foo = anno_block(gp = gpar(fill = 2:6), labels = LETTERS[1:5]))
      
      split = rep(1:5, each = 10)
      
     ht_list= Heatmap(mat2, name = "mat2", column_split = split, top_annotation = ha, 
              column_title = NULL)
      draw(ht_list)
      
      seekViewport("annotation_empty_1")
      loc1 = deviceLoc(x = unit(0, "npc"), y = unit(0, "npc"))
      seekViewport("annotation_empty_3")
      loc2 = deviceLoc(x = unit(1, "npc"), y = unit(1, "npc"))
      
      seekViewport("global")
      grid.rect(loc1$x, loc1$y, width = loc2$x - loc1$x, height = loc2$y - loc1$y, 
                just = c("left", "bottom"), gp = gpar(fill = "red"))
      grid.text("group 1", x = (loc1$x + loc2$x)*0.5, y = (loc1$y + loc2$y)*0.5)
}

gb = grid.grabExpr(make_plot())

Then you can use gb with other packages such as gtable.

[ghs101]

The solution doesn't seem to work on my machine. Do I need a special package for the function make_plot?

Error: unexpected '{' in "make_plot() {"

[jokergoo]

Sorry, that was a mistake. I have corrected it in my reply.