Barplot ComplexHeatmap

Question

I did a barplot as column annotation on a heatmap. I use ComplexHeatmap.

My input for annotation is:

vector_pvalues_adj <- c(0.3778364, 0.0001000, 0.2122000, 0.4174714, 0.3778364, 0.4799250, 0.1613250, 0.4861000, 0.4174714, 0.1008000, 0.0141000, 0.4174714, 0.0001000, 0.0018000, 0.4861000, 0.4799250, 0.0001000, 0.0001000)

And the code is:

library(ComplexHeatmap)
column_ha3 = HeatmapAnnotation("-log adj p-value"= anno_barplot(-log(vector_pvalues_adj)), gp = gpar(fill = "red"), height =  unit(20, "mm"))

I would to add an abline

abline(h = -log(0.05), col= "red")

But I'm not able, could someone suggest to me how to do it?

Yes this is the vector I used to do the barplot. dput(vector_pvalues_adj) c(0.377836363636364, 1e-04, 0.2122, 0.417471428571429, 0.377836363636364, 0.479925, 0.161325, 0.4861, 0.417471428571429, 0.1008, 0.0141, 0.417471428571429, 1e-04, 0.0018, 0.4861, 0.479925, 1e-04, 1e-04 ) — jonny jeep, Nov 03 '22 at 19:36

score 1 · Accepted Answer · answered Nov 04 '22 at 01:35

In order to add something like a horizontal line, you can use the ComplexHeatmap function decorate_annotation and the grid package.

This adds a dashed line.

library(ComplexHeatmap) # BiocManager::install("ComplexHeatmap")
library(grid)

# original code from question
vector_pvalues_adj <- c(0.3778364, 0.0001000, 0.2122000, 0.4174714, 
                        0.3778364, 0.4799250, 0.1613250, 0.4861000,
                        0.4174714, 0.1008000, 0.0141000, 0.4174714,
                        0.0001000, 0.0018000, 0.4861000, 0.4799250,
                        0.0001000, 0.0001000)

# original code from question
column_ha3 = HeatmapAnnotation(
  "-log adj p-value" = anno_barplot(-log(vector_pvalues_adj)), 
  gp = gpar(fill = "red"), height =  unit(20, "mm"))

# added for context
Heatmap(matrix(rnorm(18*18), 18), name = "mat", top_annotation = column_ha3)

# 'decorate' "-log adj p-value"
decorate_annotation("-log adj p-value", {
  grid.lines(c(.5, 18.5), c(4, 4), gp = gpar(lty = 2, col = "red"),
             default.units = "native")
})

In the last function, c(.5, 18.5) is the x-axis values, which is always equivalent to the number of columns, or 1:18 based on your data (using .5 get's you to the edges).

For y, I have it set to start at 4 and end at 4, so you get a horizontal line. in gpar I used lty = 2 which gave me a dashed line instead of the default, a solid line.)

Barplot ComplexHeatmap

1 Answers1