Plotting several heatmaps onto the same grid with the ComplexHeatmap package in R
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chriad ▴ 10
@chriad-10721
Last seen 4.0 years ago

My question is related to this one: http://stackoverflow.com/questions/13081310/combining-multiple-complex-plots-as-panels-in-a-single-figure

I also have a unsatisfactory solution based on the answer to the above questions.

I'd like a plot like this:

I use the following code for this figure:

    library(gridGraphics)
    library(grid)
    
    grab_grob <- function(){
        grid.grab()
    }
    
    drawGridHeatmap  <- function(hm) {
        draw(hm)
        grab_grob()
    }
    
    gl <- lapply(list(hm.line+ha, hm.lc+ha.nolegend, hm.dna + ha.nolegend), drawGridHeatmap)
    
    grid.newpage()
    library(gridExtra)
    grid.arrange(grobs=gl, ncol=2, clip=TRUE)

where `hm.line` etc. are `Heatmap` instances and `ha` are `HeatmapAnnotation` instances as described in the ComplexHeatmap package.

I'm aware that ComplexHeatmap is intended to draw several related Heatmaps and cluster them together. But I'd like to show several heatmaps in a grid, cluster them by themselves but they should share a common legend. Is this somehow supported in the ComplexHeatmap package?

The solution that I use has the drawback that, before plotting the heatmaps to the grid, it first plots every single heatmap on its own. How can I supress the plotting when calling `draw` in the `drawGridHeatmap` function?

complexheatmap • 11k views
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jokergoo ▴ 130
@jokergoo-8506
Last seen 7 weeks ago
Germany

First, to put heatmaps in a grid-like layout, you need to set `newpage = FALSE` in `draw()` function:

draw(hm, newpage = FALSE)

ComplexHeatmap package is only designed for arranging heatmaps horizontally, it is not easy to put heatmaps as a grid style, but there is a solution for your scenario. The solution is 1. suppressing legends for all heatmaps and use `grid.layout()` or `grid.arrange()` to arrange heatmaps in this 2x2 grid layout, 2. ComplexHeatmap can generate `Legend` objects, which means you can generate legends and add them to the plot afterwards.

In following example, I used `grid.layout()` to arrange the layout. We define a `col_fun` to make sure all three matrix use the same color mapping.

 

library(ComplexHeatmap)
library(circlize)

mat1 = matrix(rnorm(100), 10)
mat2 = matrix(rnorm(100), 10)
mat3 = matrix(rnorm(100), 10)

col_fun = colorRamp2(c(-2, 0, 2), c("blue", "white", "red"))

grid.newpage()
pushViewport(viewport(layout = grid.layout(nr = 2, nc = 2)))
pushViewport(viewport(layout.pos.row = 1, layout.pos.col = 1))
draw(Heatmap(mat1, col = col_fun, column_title = "mat1", show_heatmap_legend = FALSE), newpage = FALSE)
upViewport()

pushViewport(viewport(layout.pos.row = 1, layout.pos.col = 2))
draw(Heatmap(mat2, col = col_fun, column_title = "mat2", show_heatmap_legend = FALSE), newpage = FALSE)
upViewport()

pushViewport(viewport(layout.pos.row = 2, layout.pos.col = 1))
draw(Heatmap(mat3, col = col_fun, column_title = "mat3", show_heatmap_legend = FALSE), newpage = FALSE)
upViewport()

lgd = Legend(at = c(-2, -1, 0, 1, 2), col_fun = col_fun, title = "main matrix", title_position = "topleft")

pushViewport(viewport(layout.pos.row = 2, layout.pos.col = 2))
grid.draw(lgd)
upViewport()

upViewport()

 

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Sorry, when plotting two heatmaps with the genes with same ordering by complexheatmap, how i can put the same color scaling on the both heat maps? because one of my heat maps is darker in genes blocks =https://image.ibb.co/fbhVGo/Rplot311.png

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