R ComplexHeatmap - Adujusting the cell size in heatmap

Hi,

I aim to narrow the width of each cell and minimize the space within them. Although I attempted to do this by modifying 'width = width/2' in cell_fun1, this reduced the width but the color block did not properly fit to the cell. Any advice or solutions would be highly appreciated.

cell_fun1 = function(j, i, x, y, width, height, fill) {
  grid.rect(x = x, y = y, width = width, height = height,
            gp = gpar(col = "gray", fill = fill))
  if(mut_mat[i, j] != 0) {
    if(mut_mat[i, j] > 9) {
      grid.text(mut_mat[i, j], x, y, gp = gpar(col = "white"))
    } else {
      grid.text(mut_mat[i, j], x, y, gp = gpar(col = "black"))
    }
  }
}

col_fun1 = colorRamp2(c(0, 5, 10, 20, 40), c("white","#bae4b3","#74c476", "#31a354", "#006d2c"))


hm1 <- Heatmap(mut_mat, 
               name = "#_of_LOE_mutations",
               cluster_rows = FALSE, 
               cluster_columns = FALSE, 
               show_row_names = TRUE,
               show_column_names = TRUE,
               column_names_side = "top",
               row_names_side = "left",
               column_names_gp = gpar(fontsize=13,fontface="bold"),
               row_names_gp = gpar(fontsize=10,fontface="bold"),
               cell_fun = cell_fun1,
               col = col_fun1,
               show_heatmap_legend = FALSE,
               width = heatmap_width,
               height = heatmap_height
               )
hm1

Original heatmap:

enter image description here

After modifying "width = width" to "width = width/2" in cell_fun1

enter image description here

r complexheatmap

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updated 2.7 years ago by jv

• written 2.7 years ago by TC_Chang •

I may be missing something, but can you not just shrink the width of the heatmap in general? That is how one would typically do this.

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written 2.7 years ago by jared.andrews07

How are you setting heatmap_width and heatmap_height? That's what you'll need to tweak.

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written 2.7 years ago by Ram

1 answer

I think the main thing is not to use "width = width/2" in cell_fun1. Using ComplexHeatmap 2.14.0 on R 4.2.1 i was able to modify cell width and height via width and height params in call to Heatmap. I tried a few different widths and heights and each time the cell borders adjusted accordingly.

cell_fun1 = function(j, i, x, y, width, height, fill) {
  grid.rect(x = x, y = y, width = width, height = height,
            gp = gpar(col = "gray", fill = fill))
  if(mat[i, j] != 0) {
    if(mat[i, j] > 9) {
      grid.text(mat[i, j], x, y, gp = gpar(col = "white"))
    } else {
      grid.text(mat[i, j], x, y, gp = gpar(col = "black"))
    }
  }
}

mat <- matrix(c(0,25,0,1,12,2,9,1,4,3,1,12,3,0,1), byrow = TRUE, nrow = 3)
rownames(mat) <- c("KRAS", "ARID1A", "PIK3CA")

library(ComplexHeatmap)
col_fun1 = circlize::colorRamp2 (c(0, 5, 10, 20, 40), 
                                 c("white","#bae4b3","#74c476", "#31a354", "#006d2c"))

hm1 <- Heatmap(mat, 
               name = "#_of_LOE_mutations",
               cluster_rows = FALSE, 
               cluster_columns = FALSE, 
               show_row_names = TRUE,
               show_column_names = TRUE,
               column_names_side = "top",
               row_names_side = "left",
               column_names_gp = gpar(fontsize=13,fontface="bold"),
               row_names_gp = gpar(fontsize=10,fontface="bold"),
               cell_fun = cell_fun1,
               col = col_fun1,
               show_heatmap_legend = FALSE,
               width = unit(5, "cm"),
               height = unit(2, "cm")
)
hm1

enter image description here

The only difference in my code and yours is that I explicitly set width and height using unit since you didn't show how you defined heatmap_width and heatmap_height in your example.

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written 2.7 years ago by jv