Diagonal heatmap

[ekaterinaesenkova]

Good day!

Is there a possibility for a diagonal heatmap ( to have only upper/lower triangular of it plotted)?

Thanks in advance!

[jokergoo]

Check this example code:

m = matrix(rnorm(100), 10)
cm = cor(m)

od =  hclust(dist(cm))$order

cm = cm[od, od]

Heatmap(cm, rect_gp = gpar(type = "none"), cluster_rows = FALSE, cluster_columns = FALSE,
	cell_fun = function(j, i, x, y, w, h, fill) {
		if(i >= j) {
			grid.rect(x, y, w, h, gp = gpar(fill = fill, col = fill))
		}
	})

One thing needs to be noted: Here we compare the row index and column index in cell_fun, this requires the matrix for Heatmap() (which is cm) is already reordered by clustering before sending to heatmap.

[ekaterinaesenkova]

Thank you! One more question: is there a possibility to keep dendrograms, previously created by hclust (as cluster_rows = FALSE, cluster_columns = FALSE)?

Thanks in advance!

[jokergoo]

Then I think you can directly compare x and y which are the physical locations in the heatmap body. In this case, you don't need to pre-order the matrix and instead, you can apply clustering to the matrix:

m = matrix(rnorm(100), 10)
cm = cor(m)

Heatmap(cm, rect_gp = gpar(type = "none"), column_dend_side = "bottom",
	cell_fun = function(j, i, x, y, w, h, fill) {
		if(as.numeric(x) <= 1 - as.numeric(y)) {
			grid.rect(x, y, w, h, gp = gpar(fill = fill, col = fill))
		}
	})

[ekaterinaesenkova]

Thank you! Another problem I encountered - when I create ht_list to combine the diagonal matrices, it takes just row annotation from my h1 and duplicates it on my h2 side as well, so my original row annotation for h2 is overwritten. (see the image: the right side should be the same as upper annotation). Is there a way to solve this? Thanks in advance!

[jokergoo]

Can you also attach the code? The following is what I have tried and it works fine.

library(ComplexHeatmap)
m = cor(matrix(rnorm(100), 10))

library(circlize)
col1 = colorRamp2(c(-1, 0, 1), c("green", "black", "red"))
col2 = colorRamp2(c(-1, 0, 1), c("purple", "white", "orange"))

od =  hclust(dist(m))$order
m2 = m[od, od]

ht1 = Heatmap(m2, rect_gp = gpar(type = "none"), col = col1,
    cluster_rows = FALSE, cluster_columns = FALSE,
    bottom_annotation = HeatmapAnnotation(foo1 = 1:10),
    left_annotation = rowAnnotation(bar1 = 1:10),
    cell_fun = function(j, i, x, y, w, h, fill) {
        if(i >= j) {
            grid.rect(x, y, w, h, gp = gpar(fill = fill, col = fill))
        }
    })

ht2 = Heatmap(m2, rect_gp = gpar(type = "none"), col = col2,
    cluster_rows = FALSE, cluster_columns = FALSE,
    top_annotation = HeatmapAnnotation(foo2 = rep(c("a", "b"), each = 5)),
    right_annotation = rowAnnotation(bar2 = rep(c("a", "b"), each = 5)),
    cell_fun = function(j, i, x, y, w, h, fill) {
        if(i <= j) {
            grid.rect(x, y, w, h, gp = gpar(fill = fill, col = fill))
        }
    })

draw(ht1 + ht2, ht_gap = unit(-70, "mm"))

[ekaterinaesenkova]

Thanks for the response! Below is my code for annotation for my genomic and metabolic distance matrices. I noticed that if I change the order of ht_list= h1 + h2 to ht_list= h2 + h1, I get annotation of rows for h2. Thanks in advance!

#genomic 
column_ha = HeatmapAnnotation(Phylum = as.factor(phylum),
col = list(Phylum = c(Actinobacteria ="#0F02C2", Bacteroidetes = "#3C9953", Firmicutes = "#FFED7D", Proteobacteria = "#C22741")), show_legend = c("Phylum" = FALSE), border = TRUE)

row_ha = rowAnnotation(Phylum = as.factor(phylum), Class = as.factor(class),Gsize=anno_points(as.numeric(Gsize)), col = list(Phylum = c( Actinobacteria ="#0F02C2", Bacteroidetes = "#3C9953", 
Firmicutes = "#FFED7D", Proteobacteria = "#C22741"), Class = c(Actinomycetia="#0F02C2", Bacilli="#1CEFFF", Bacteroidia="#3C9953", Clostridia="#FFED7D", Coriobacteriia="#D20AFF",Erysipelotrichia="#C22741", Gammaproteobacteria="#FFC2FA")), show_legend = c("Phylum" = FALSE, "Class" = FALSE),  border = TRUE)

col_fun = colorRamp2(c(0, 0.5, 1), c("white", "grey","black"))


h1=Heatmap(as.matrix(gen_dist), rect_gp = gpar(type = "none"), column_dend_side = "bottom", name = "Genomic similarity", bottom_annotation = column_ha, left_annotation = row_ha,
           heatmap_legend_param = list(direction = "horizontal",side="top"),
           col=col_fun,
           cell_fun = function(j, i, x, y, w, h, fill) {
             if(as.numeric(x) <= 1 - as.numeric(y) + 1e-6) {
               grid.rect(x, y, w, h, gp = gpar(fill = fill, col = fill))
             }
           })

#metabolic

column_ha = HeatmapAnnotation(Phylum = as.factor(phylum), 
col = list(Phylum = c(Actinobacteria ="#0F02C2", Bacteroidetes = "#3C9953", Firmicutes = "#FFED7D", Proteobacteria = "#C22741")),border = TRUE)
row_ha= rowAnnotation(Phylum = as.factor(phylum), Class = as.factor(class),  
col = list(Phylum2 = c(Actinobacteria ="#0F02C2", Bacteroidetes = "#3C9953", Firmicutes = "#FFED7D", Proteobacteria = "#C22741"), Class2 = c(Actinomycetia="#0F02C2", Bacilli="#1CEFFF", Bacteroidia = "#3C9953", Clostridia="#FFED7D", Coriobacteriia="#D20AFF", Erysipelotrichia="#C22741",Gammaproteobacteria="#FFC2FA")),show_legend = c("Phylum" = FALSE, "Class" = TRUE),border = TRUE)

h2=Heatmap(as.matrix(met_dist), rect_gp = gpar(type = "none"), column_dend_side = "top",row_dend_side = "right", 
           name = "Metabolic distance", top_annotation = column_ha, right_annotation = row_ha,
           col=col_fun, heatmap_legend_param = list(direction = "horizontal",side="right"),
           cell_fun = function(j, i, x, y, w, h, fill) {
             if(as.numeric(x) >= 1 - as.numeric(y) + 1e-6) {
               grid.rect(x, y, w, h, gp = gpar(fill = fill, col = fill))
             }
           })


ht_list = h1+h2
draw(ht_list,annotation_legend_side = "bottom", heatmap_legend_side = "bottom",ht_gap = unit(-47, "cm"))

[jokergoo]

If you change to h2 + h1, then you should also change the settings in the two heatmaps, i.e., change top_annotation to bottom_annotation in h2, and right_annotation to left_annotation in h2. The direction of the comparisons in two cell_fun should also be reversed.

[ekaterinaesenkova]

thank you!

[Sbzahedi]

Good day! Is it possible to split in diagonal while keeping cluster_rows and cluster_columns as true?

[Sbzahedi]

Here is my code so far:

corr_mx <- round(cor(log10(map + 1)), 2)
coul <- rev(colorRampPalette(brewer.pal(8, "Spectral"))(25))

row_dend <- hclust(dist(corr_mx))
column_dend <- hclust(dist(t(corr_mx)))

row_cut <- cutree(row_dend, h = 0.5max(row_dend$height))
column_cut <- cutree(column_dend, h = 0.5max(column_dend$height))

hm <- Heatmap(as.matrix(corr_mx), col = coul,
heatmap_legend_param = list(title = "Legend", direction = "horizontal"),
cluster_rows = TRUE, cluster_columns = TRUE,
row_split = row_cut, column_split = column_cut,
row_names_gp = gpar(fontsize = 2), column_names_gp = gpar(fontsize = 2),
column_title = "HEATMAP",
column_title_gp = gpar(fontsize = 15, fontface = "bold"),
column_title_side = "bottom",
show_column_dend = FALSE, show_row_names = FALSE, row_dend_width = unit(1, "cm"),
row_gap = unit(0.5, "mm"), column_gap = unit(0.5, "mm"),
layer_fun = function(j, i, x, y, width, height, fill, slice_r, slice_c) {
v = pindex(corr_mx, i, j)
if (slice_r == slice_c) {
grid.rect(gp = gpar(lwd = 1.5, fill = "transparent"))}}
)
draw(hm, heatmap_legend_side = "bottom")

[sotuamax]

Greetings!

I try to draw a very large matrix in triangle form using Heatmap cell_fun. However, it takes long time to draw it. I checked the document, and layer_fun is a vectorized version of cell_fun and may runs faster. Is that possible to provide a example code here to draw triangle heatmap using layer_fun?

Many thanks.

Best,

[jokergoo]

Can you also provide some example data and code?

[sotuamax]

Hello,

I attached a subset data here.
counts.txt

The code I used to draw a triangle heatmap in a faster way (cell_fun works but is very slow):

mat <- read.table("counts.txt", sep = "\t", header = F) |> as.matrix()
col_fun <- colorRamp2(c(1, 3, 5, 8, 10), c("white", "#FBB91F", "#F17020", "#C43C4E", "#9C2964FF"))
Heatmap(log2(mat+1),
name = "ht1",
rect_gp = gpar(type = "none"),
cluster_rows = F,
cluster_columns = F,
show_row_dend = F,
show_column_dend = F,
show_column_names = F,
show_row_names = F,
col = col_fun,
border = T,
show_heatmap_legend = F,
width = unit(0.8, "snpc"),
height = unit(0.8, "snpc"),
layer_fun = function(j, i, x, y, width, height, fill) {
v = pindex(mat, i, j)
if (v[i, ] < v[, j]) {
grid.rect(gp = gpar(lwd = 1.5, fill = fill, col = fill))}}
)

I also try to rotate the triangle heatmap and save it to a pdf file (like below).

However, in reference to #186, it doesn't show well. Is there any better way to
do it?

The plot is for a HiC related, and I called topological associated domain (TAD) from other source, and annotated the region. I can mark the TAD use square like below. Is there any way to mark it triangle of TAD?

Thank you so much!

Best,

[jokergoo]

I will use the mat[100, 100] for demonstration.

Heatmap(log2(mat[1:100, 1:100]+1),
	name = "ht1",
	rect_gp = gpar(type = "none"),
	cluster_rows = F,
	cluster_columns = F,
	show_row_dend = F,
	show_column_dend = F,
	show_column_names = F,
	show_row_names = F,
	col = col_fun,
	border = T,
	show_heatmap_legend = F,
	width = unit(0.8, "snpc"),
	height = unit(0.8, "snpc"),
	layer_fun = function(j, i, x, y, width, height, fill) {
		l = i >= j
		grid.rect(x[l], y[l], width[l], height[l], gp = gpar(lwd = 1.5, fill = fill[l], col = fill[l]))
	}
)

As in layer_fun, all arguments are vectors, to only draw the triangle, e.g. the lower triangle, you just need to use the values where i >= j.

To rotate the plot by 45 degrees, you can simply push a global viewport with 45 degrees rotation:

ht = Heatmap(log2(mat[1:100, 1:100]+1),
	name = "ht1",
	rect_gp = gpar(type = "none"),
	cluster_rows = F,
	cluster_columns = F,
	show_row_dend = F,
	show_column_dend = F,
	show_column_names = F,
	show_row_names = F,
	col = col_fun,
	border = T,
	show_heatmap_legend = F,
	width = unit(0.8, "snpc"),
	height = unit(0.8, "snpc"),
	layer_fun = function(j, i, x, y, width, height, fill) {
		l = i >= j
		grid.rect(x[l], y[l], width[l], height[l], gp = gpar(lwd = 1.5, fill = fill[l], col = fill[l]))
	}
)

grid.newpage()
pushViewport(viewport(angle = 45, width = 1/sqrt(2), height = 1/sqrt(2)))
draw(ht, newpage = FALSE)
popViewport()

[sotuamax]

Thank you so much for your prompt response.

It works!

Best,
Meiyuan