Table of Contents

Heatmap Annotations

Author: Zuguang Gu ( z.gu@dkfz.de )

Date: 2017-11-01


The annotation graphics actually are quite general. The only common characteristic for annotations is that they are aligned to the columns or rows of the heatmap. Here there is a HeatmapAnnotation class which is used to define annotations on columns or rows.

Column annotation

Simple annotation

A simple annotation is defined as a vector which contains discrete classes or continuous values. Since the simple annotation is represented as a vector, multiple simple annotations can be specified as a data frame. Colors for the simple annotations can be specified by col with a vector or color mapping functions, depending on whether the simple annotations are discrete or continuous.

In the heatmap, simple annotations will be represented as rows of grids.

There is a draw() method for the HeatmapAnnotation class. draw() is used internally and here we just use it for demonstration.

library(ComplexHeatmap)
library(circlize)

df = data.frame(type = c(rep("a", 5), rep("b", 5)))
ha = HeatmapAnnotation(df = df)
ha
## A HeatmapAnnotation object with 1 annotation.
## 
## An annotation with discrete color mapping
## name: type 
## position: column 
## show legend: TRUE
draw(ha, 1:10)

plot of chunk heatmap_annotation

The color of simple annotation should be specified as a list with names for which names in the color list (here it is type in following example) correspond to the names in the data frame. Each color vector should better has names as well to map to the levels of annotations.

ha = HeatmapAnnotation(df = df, col = list(type = c("a" =  "red", "b" = "blue")))
ha
## A HeatmapAnnotation object with 1 annotation.
## 
## An annotation with discrete color mapping
## name: type 
## position: column 
## show legend: TRUE
draw(ha, 1:10)

plot of chunk heatmap_annotation_col

For continuous annotation, colors should be a color mapping function.

ha = HeatmapAnnotation(df = data.frame(age = sample(1:20, 10)),
    col = list(age = colorRamp2(c(0, 20), c("white", "red"))))
ha
## A HeatmapAnnotation object with 1 annotation.
## 
## An annotation with continuous color mapping
## name: age 
## position: column 
## show legend: TRUE
draw(ha, 1:10)

plot of chunk heatmap_annotation_colfun

Color for NA can be set by na_col:

df2 = data.frame(type = c(rep("a", 5), rep("b", 5)),
                age = sample(1:20, 10))
df2$type[5] = NA
df2$age[5] = NA
ha = HeatmapAnnotation(df = df2, 
  col = list(type = c("a" =  "red", "b" = "blue"),
             age = colorRamp2(c(0, 20), c("white", "red"))),
  na_col = "grey")
draw(ha, 1:10)

plot of chunk unnamed-chunk-1

Put more than one annotations by a data frame.

df = data.frame(type = c(rep("a", 5), rep("b", 5)),
                age = sample(1:20, 10))
ha = HeatmapAnnotation(df = df,
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red")))
)
ha
## A HeatmapAnnotation object with 2 annotations.
## 
## An annotation with discrete color mapping
## name: type 
## position: column 
## show legend: TRUE 
## 
## An annotation with continuous color mapping
## name: age 
## position: column 
## show legend: TRUE
draw(ha, 1:10)

plot of chunk heatmap_annotation_mixed

Also individual annotations can be directly specified as vectors:

ha = HeatmapAnnotation(type = c(rep("a", 5), rep("b", 5)),
                       age = sample(1:20, 10),
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red")))
)
ha
## A HeatmapAnnotation object with 2 annotations.
## 
## An annotation with discrete color mapping
## name: type 
## position: column 
## show legend: TRUE 
## 
## An annotation with continuous color mapping
## name: age 
## position: column 
## show legend: TRUE
draw(ha, 1:10)

plot of chunk heatmap_annotation_vector

To put column annotation to the heatmap, specify top_annotation and bottom_annotation in Heatmap().

ha1 = HeatmapAnnotation(df = df,
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red")))
)
ha2 = HeatmapAnnotation(df = data.frame(age = sample(1:20, 10)),
    col = list(age = colorRamp2(c(0, 20), c("white", "red"))))

set.seed(123)
mat = matrix(rnorm(80, 2), 8, 10)
mat = rbind(mat, matrix(rnorm(40, -2), 4, 10))
rownames(mat) = paste0("R", 1:12)
colnames(mat) = paste0("C", 1:10)

Heatmap(mat, top_annotation = ha1, bottom_annotation = ha2)

plot of chunk heatmap_column_annotation

Complex annotations

Besides simple annotations, there are complex annotations. The complex annotations are always represented as self-defined graphic functions. Actually, for each column annotation, there will be a viewport created waiting for graphics. The annotation function here defines how to put the graphics to this viewport. The only argument of the function is an index of column which is already adjusted by column clustering.

In following example, an annotation of points is created. Please note how we define xscale so that positions of points correspond to middle points of the columns if the annotation is added to the heatmap.

value = rnorm(10)
column_anno = function(index) {
    n = length(index)
    # since middle of columns are in 1, 2, ..., n and each column has width 1
    # then the most left should be 1 - 0.5 and the most right should be n + 0.5
    pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = range(value)))
    # since order of columns will be adjusted by clustering, here we also 
    # need to change the order by `[index]`
    grid.points(index, value[index], pch = 16, default.unit = "native")
    # this is very important in order not to mess up the layout
    upViewport() 
}
ha = HeatmapAnnotation(points = column_anno)  # here the name is arbitrary
ha
## A HeatmapAnnotation object with 1 annotation.
## 
## An annotation with self-defined function
## name: points 
## position: column
draw(ha, 1:10)

plot of chunk heatmap_annotation_complex

Above code is only for demonstration. You don't realy need to define a points annotation, there are already several annotation generators provided in the package such as anno_points() or anno_barplot() which generate such complex annotation function:

The input value for these anno_* functions is quite straightforward. It should be a numeric vector (e.g. for anno_points() and anno_barplot()), a matrix or list (for anno_boxplot(), anno_histogram() or anno_density()), or a character vector (for anno_text()).

ha = HeatmapAnnotation(points = anno_points(value))
draw(ha, 1:10)

plot of chunk heatmap_annotation_points

ha = HeatmapAnnotation(barplot = anno_barplot(value))
draw(ha, 1:10)

plot of chunk heatmap_annotation_barplot

anno_boxplot() generates boxplot for each column in the matrix.

ha = HeatmapAnnotation(boxplot = anno_boxplot(mat))
draw(ha, 1:10)

plot of chunk heatmap_annotation_boxplot

You can mix simple annotations and complex annotations:

ha = HeatmapAnnotation(df = df, 
                       points = anno_points(value),
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red"))))
ha
## A HeatmapAnnotation object with 3 annotations.
## 
## An annotation with discrete color mapping
## name: type 
## position: column 
## show legend: TRUE 
## 
## An annotation with continuous color mapping
## name: age 
## position: column 
## show legend: TRUE 
## 
## An annotation with self-defined function
## name: points 
## position: column
draw(ha, 1:10)

plot of chunk heatmap_annotation_mixed_with_complex

Since simple annotations can also be specified as vectors, actually you arrange annotations in any order:

ha = HeatmapAnnotation(type = c(rep("a", 5), rep("b", 5)),
                       points = anno_points(value),
                       age = sample(1:20, 10), 
                       bars = anno_barplot(value),
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red"))))
ha
## A HeatmapAnnotation object with 4 annotations.
## 
## An annotation with discrete color mapping
## name: type 
## position: column 
## show legend: TRUE 
## 
## An annotation with self-defined function
## name: points 
## position: column 
## 
## An annotation with continuous color mapping
## name: age 
## position: column 
## show legend: TRUE 
## 
## An annotation with self-defined function
## name: bars 
## position: column
draw(ha, 1:10)

plot of chunk unnamed-chunk-2

For some of the anno_* functions, graphic parameters can be set by gp argument. Also note how we specify baseline in anno_barplot().

ha = HeatmapAnnotation(barplot1 = anno_barplot(value, baseline = 0, gp = gpar(fill = ifelse(value > 0, "red", "green"))),
                       points = anno_points(value, gp = gpar(col = rep(1:2, 5))),
                       barplot2 = anno_barplot(value, gp = gpar(fill = rep(3:4, 5))))
ha
## A HeatmapAnnotation object with 3 annotations.
## 
## An annotation with self-defined function
## name: barplot1 
## position: column 
## 
## An annotation with self-defined function
## name: points 
## position: column 
## 
## An annotation with self-defined function
## name: barplot2 
## position: column
draw(ha, 1:10)

plot of chunk heatmap_annotation_anno_gp

If there are more than one annotations, you can control height of each annotation by annotation_height. The value of annotation_height can either be numeric values or unit objects.

# set annotation height as relative values
ha = HeatmapAnnotation(df = df, points = anno_points(value), boxplot = anno_boxplot(mat),
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red"))),
    annotation_height = c(1, 2, 3, 4))
draw(ha, 1:10)

plot of chunk unnamed-chunk-3

# set annotation height as absolute units
ha = HeatmapAnnotation(df = df, points = anno_points(value), boxplot = anno_boxplot(mat),
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red"))),
    annotation_height = unit.c((unit(1, "npc") - unit(4, "cm"))*0.5, (unit(1, "npc") - unit(4, "cm"))*0.5, 
        unit(2, "cm"), unit(2, "cm")))
draw(ha, 1:10)

plot of chunk unnamed-chunk-4

With the annotation constructed, you can assign to the heatmap either by top_annotation or bottom_annotation. Also you can control the size of total column annotations by top_annotation_height and bottom_annotation_height if the height of the annotations are relative values.

If the annotation has proper size (high enough), it would be helpful to add axis on it. anno_points(), anno_barplot() and anno_boxplot() support axes. Please note we didn't pre-allocate space for axes particularly, we only assume there are already empty spaces for showing axes.

ha = HeatmapAnnotation(df = df, points = anno_points(value),
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red"))))
ha_boxplot = HeatmapAnnotation(boxplot = anno_boxplot(mat, axis = TRUE))
Heatmap(mat, name = "foo", top_annotation = ha, bottom_annotation = ha_boxplot, 
    bottom_annotation_height = unit(3, "cm"))

plot of chunk add_annotation

Gaps below each annotation can be specified by gap in HeatmapAnnotation().

ha = HeatmapAnnotation(df = df, points = anno_points(value), gap = unit(c(2, 4), "mm"),
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red"))))
Heatmap(mat, name = "foo", top_annotation = ha)

plot of chunk unnamed-chunk-5

You can suppress some of the annotation legend by specifying show_legend to FALSE when creating the HeatmapAnnotation object.

ha = HeatmapAnnotation(df = df, show_legend = c(FALSE, TRUE),
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red"))))
Heatmap(mat, name = "foo", top_annotation = ha)

plot of chunk annotation_show

More types of annotations which show data distribution in corresponding columns are supported by anno_histogram() and anno_density().

ha_mix_top = HeatmapAnnotation(histogram = anno_histogram(mat, gp = gpar(fill = rep(2:3, each = 5))),
    density_line = anno_density(mat, type = "line", gp = gpar(col = rep(2:3, each = 5))),
    violin = anno_density(mat, type = "violin", gp = gpar(fill = rep(2:3, each = 5))),
    heatmap = anno_density(mat, type = "heatmap"))
Heatmap(mat, name = "foo", top_annotation = ha_mix_top, top_annotation_height = unit(8, "cm"))

plot of chunk annotation_more

Text is also one of the annotaiton graphics. anno_text() supports adding text as heatmap annotations. With this annotation function, it is easy to simulate column names with rotations. Note you need to calcualte the space for the text annotations by hand and the package doesn't garentee that all the rotated text are shown in the plot (In following figure, if row names and legend are not drawn, 'C10C10C10' will show completely, but there are some tricks which can be found in the Examples vignette).

long_cn = do.call("paste0", rep(list(colnames(mat)), 3))  # just to construct long text
ha_rot_cn = HeatmapAnnotation(text = anno_text(long_cn, rot = 45, just = "left", offset = unit(2, "mm")))
Heatmap(mat, name = "foo", top_annotation = ha_rot_cn, top_annotation_height = unit(2, "cm"))

plot of chunk rotated_column_names

Row annotations

Row annotation is also defined by the HeatmapAnnotation class, but with specifying which to row.

df = data.frame(type = c(rep("a", 6), rep("b", 6)))
ha = HeatmapAnnotation(df = df, col = list(type = c("a" = "red", "b" = "blue")),
    which = "row", width = unit(1, "cm"))
draw(ha, 1:12)

plot of chunk row_annotation

There is a helper function rowAnnotation() which is same as HeatmapAnnotation(..., which = "row").

ha = rowAnnotation(df = df, col = list(type = c("a" = "red", "b" = "blue")), width = unit(1, "cm"))

anno_* functions also works for row annotations, by you need to add which = "row" in the function. E.g:

ha = rowAnnotation(points = anno_points(runif(10), which = "row"))

Similar as rowAnnotation(), there are corresponding wrapper anno_* functions. There functions are almost same as the original functions except pre-defined which argument to row.

Similar, there can be more than one row annotations.

ha_combined = rowAnnotation(df = df, boxplot = row_anno_boxplot(mat), 
    col = list(type = c("a" = "red", "b" = "blue")),
    annotation_width = c(1, 3))
draw(ha_combined, 1:12)

plot of chunk unnamed-chunk-8

Mix heatmaps and row annotations

Essentially, row annotations and column annotations are identical graphics, but in practice, there is some difference. In ComplexHeatmap package, row annotations have the same place as the heatmap while column annotations are just like accessory components of heatmaps. The idea here is that row annotations can be corresponded to all the heatmaps in the list while column annotations can only be corresponded to its own heatmap. For row annotations, similar as heatmaps, you can append the row annotations to heatmap or heatmap list or even row annotation object itself. The order of elements in row annotations will be adjusted by the clustering of heatmaps.

ha = rowAnnotation(df = df, col = list(type = c("a" = "red", "b" = "blue")),
    width = unit(1, "cm"))
ht1 = Heatmap(mat, name = "ht1")
ht2 = Heatmap(mat, name = "ht2")
ht1 + ha + ht2

plot of chunk heatmap_list_with_row_annotation

If km or split is set in the main heatmap, the row annotations are splitted as well.

ht1 = Heatmap(mat, name = "ht1", km = 2)
ha = rowAnnotation(df = df, col = list(type = c("a" = "red", "b" = "blue")),
    boxplot = row_anno_boxplot(mat, axis = TRUE), 
    annotation_width = unit(c(1, 5), "cm"))
ha + ht1

plot of chunk heatmap_list_with_row_annotation_complex

When row split is applied, graphical parameters for annotation function can be specified as with the same length as the number of row slices.

ha = rowAnnotation(boxplot = row_anno_boxplot(mat, gp = gpar(fill = c("red", "blue"))), 
    width = unit(2, "cm"))
ha + ht1

plot of chunk heatmap_list_with_row_annotation_graphical_parameter

Since only row clustering and row titles for the main heatmap are kept, they can be adjusted to the most left or right side of the plot by setting row_hclust_side and row_sub_title_side:

draw(ha + ht1, row_dend_side = "left", row_sub_title_side = "right")

plot of chunk heatmap_list_hclust_title_side

Self define row annotations

Self-defining row annotations is same as self-defining column annotations. The only difference is that x coordinate and y coordinate are switched. If row annotations are split by rows, the argument index will automatically be the index in the 'current' row slice.

value = rowMeans(mat)
row_anno = function(index) {
    n = length(index)
    pushViewport(viewport(xscale = range(value), yscale = c(0.5, n + 0.5)))
    grid.rect()
    # recall row order will be adjusted, here we specify `value[index]`
    grid.points(value[index], seq_along(index), pch = 16, default.unit = "native")
    upViewport()
}
ha = rowAnnotation(points = row_anno, width = unit(1, "cm"))
ht1 + ha

plot of chunk unnamed-chunk-9

For the self-defined annotation function, there can be a second argument k which gives the index of 'current' row slice.

row_anno = function(index, k) {
    n = length(index)
    col = c("blue", "red")[k]
    pushViewport(viewport(xscale = range(value), yscale = c(0.5, n + 0.5)))
    grid.rect()
    grid.points(value[index], seq_along(index), pch = 16, default.unit = "native", gp = gpar(col = col))
    upViewport()
}
ha = rowAnnotation(points = row_anno, width = unit(1, "cm"))
ht1 + ha

plot of chunk unnamed-chunk-10

Heatmap with zero row

If you only want to visualize meta data of your matrix, you can set the matrix with zero row. In this case, only one heatmap is allowed.

ha = HeatmapAnnotation(df = data.frame(value = runif(10), type = rep(letters[1:2], 5)),
    barplot = anno_barplot(runif(10)),
    points = anno_points(runif(10)))
zero_row_mat = matrix(nrow = 0, ncol = 10)
colnames(zero_row_mat) = letters[1:10]
Heatmap(zero_row_mat, top_annotation = ha, column_title = "only annotations")

plot of chunk zero_row_heatmap

This feature is very useful if you want to compare multiple metrics. Axes and labels in following plot are added by heatmap decoration. Also notice how we adjust paddings of the plotting regions to give enough space for hte axis labels.

ha = HeatmapAnnotation(df = data.frame(value = runif(10), type = rep(letters[1:2], 5)),
    barplot = anno_barplot(runif(10), axis = TRUE),
    points = anno_points(runif(10), axis = TRUE),
    annotation_height = unit(c(0.5, 0.5, 4, 4), "cm"))
zero_row_mat = matrix(nrow = 0, ncol = 10)
colnames(zero_row_mat) = letters[1:10]
ht = Heatmap(zero_row_mat, top_annotation = ha, column_title = "only annotations")
draw(ht, padding = unit(c(2, 20, 2, 2), "mm"))
decorate_annotation("value", {grid.text("value", unit(-2, "mm"), just = "right")})
decorate_annotation("type", {grid.text("type", unit(-2, "mm"), just = "right")})
decorate_annotation("barplot", {
    grid.text("barplot", unit(-10, "mm"), just = "bottom", rot = 90)
    grid.lines(c(0, 1), unit(c(0.2, 0.2), "native"), gp = gpar(lty = 2, col = "blue"))
})
decorate_annotation("points", {
    grid.text("points", unit(-10, "mm"), just = "bottom", rot = 90)
})

plot of chunk unnamed-chunk-11

Heatmap with zero column

If no heatmap is needed to draw and users only want to arrange a list of row annotations, an empty matrix with no column can be added to the heatmap list. Within the zero-column matrix, you can either split row annotaitons:

ha_boxplot = rowAnnotation(boxplot = row_anno_boxplot(mat), width = unit(3, "cm"))
ha = rowAnnotation(df = df, col = list(type = c("a" = "red", "b" = "blue")), width = unit(2, "cm"))
text = paste0("row", seq_len(nrow(mat)))
ha_text = rowAnnotation(text = row_anno_text(text), width = max_text_width(text))
nr = nrow(mat)
Heatmap(matrix(nrow = nr, ncol = 0), split = sample(c("A", "B"), nr, replace = TRUE)) + 
    ha_boxplot + ha + ha_text

plot of chunk all_row_annotations

or add dendrograms to the row annotations:

dend = hclust(dist(mat))
Heatmap(matrix(nrow = nr, ncol = 0), cluster_rows = dend) + 
    ha_boxplot + ha + ha_text

plot of chunk no_heatmap_but_with_cluster

Remember it is not allowed to only concantenate row annotations because row annotations don't provide information of number of rows.

Use heatmap instead of simple row annotations

Finally, if your row annotations are simple annotations, I recommand to use heatmap instead. Following two methods generate similar figures.

df = data.frame(type = c(rep("a", 6), rep("b", 6)))
Heatmap(mat) + rowAnnotation(df = df, col = list(type = c("a" = "red", "b" = "blue")), 
    width = unit(1, "cm"))

plot of chunk unnamed-chunk-12

Heatmap(mat) + Heatmap(df, name = "type", col = c("a" = "red", "b" = "blue"), 
    width = unit(1, "cm"))

plot of chunk unnamed-chunk-12

Axes for annotations

Axes for complex annotations are important to show range and direction of the data. anno_* functions provide axis and axis_side arguments to control the axes.

ha1 = HeatmapAnnotation(b1 = anno_boxplot(mat, axis = TRUE),
    p1 = anno_points(colMeans(mat), axis = TRUE))
ha2 = rowAnnotation(b2 = row_anno_boxplot(mat, axis = TRUE),
    p2 = row_anno_points(rowMeans(mat), axis = TRUE), width = unit(2, "cm"))
Heatmap(mat, top_annotation = ha1, top_annotation_height = unit(2, "cm")) + ha2

plot of chunk unnamed-chunk-13

For row annotations, by default direction of the data is from left to right. But it may confuse people if the row annotation is placed on the left of the heatmap. You can change axis directions for row annotations by axis_direction. Compare following two plots:

pushViewport(viewport(layout = grid.layout(nr = 1, nc = 2)))
pushViewport(viewport(layout.pos.row = 1, layout.pos.col = 1))
ha = rowAnnotation(boxplot = row_anno_boxplot(mat, axis = TRUE), width = unit(3, "cm"))
ht_list = ha + Heatmap(mat)
draw(ht_list, column_title = "normal axis direction", newpage = FALSE)
upViewport()

pushViewport(viewport(layout.pos.row = 1, layout.pos.col = 2))
ha = rowAnnotation(boxplot = row_anno_boxplot(mat, axis = TRUE, axis_direction = "reverse"), 
    width = unit(3, "cm"))
ht_list = ha + Heatmap(mat)
draw(ht_list, column_title = "reverse axis direction", newpage = FALSE)
upViewport(2)

plot of chunk unnamed-chunk-14

Stacked barplots

Barplot annotation can be stacked barplots if the input (let's say x) is a matrix with columns larger than one. In this case, if graphic parameters are specified as a vector, the length can only be one or the number of columns in x. Since barplots are stacked, each row can only have all positive values or all negative values.

Note the drawback is there is no legend for the stacked barplots, you need to generate it manually (check this section)

foo1 = matrix(abs(rnorm(20)), ncol = 2)
foo1[1, ] = -foo1[1, ]
column_ha = HeatmapAnnotation(foo1 = anno_barplot(foo1, axis = TRUE))
foo2 = matrix(abs(rnorm(24)), ncol = 2)
row_ha = rowAnnotation(foo2 = row_anno_barplot(foo2, axis = TRUE, axis_side = "top",
    gp = gpar(fill = c("red", "blue"))), width = unit(2, "cm"))
Heatmap(mat, top_annotation = column_ha, top_annotation_height = unit(2, "cm"), km = 2) + row_ha

plot of chunk unnamed-chunk-15

Add annotation names

From version 1.11.5, HeatmapAnnotation() supports adding annotation names directly to the annotations. However, due to the design of the package, sometimes the names will be positioned outside of the plot or overlap to other heatmap compoments, thus, by default it is turned off.

df = data.frame(type = c(rep("a", 5), rep("b", 5)),
                age = sample(1:20, 10))
value = rnorm(10)
ha = HeatmapAnnotation(df = df, points = anno_points(value, axis = TRUE),
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red"))),
    annotation_height = unit(c(0.5, 0.5, 2), "cm"),
    show_annotation_name = TRUE,
    annotation_name_offset = unit(2, "mm"),
    annotation_name_rot = c(0, 0, 90))
Heatmap(mat, name = "foo", top_annotation = ha)

plot of chunk unnamed-chunk-16

Or the row annotation names: Note we manually adjust padding to fully show the text of “points”.

df = data.frame(type = c(rep("a", 6), rep("b", 6)),
                age = sample(1:20, 12))
value = rnorm(12)
ha = rowAnnotation(df = df, points = row_anno_points(value, axis = TRUE),
    col = list(type = c("a" = "red", "b" = "blue"),
               age = colorRamp2(c(0, 20), c("white", "red"))),
    annotation_width = unit(c(0.5, 0.5, 2), "cm"),
    show_annotation_name = c(TRUE, FALSE, TRUE),
    annotation_name_offset = unit(c(2, 2, 8), "mm"),
    annotation_name_rot = c(90, 90, 0))
ht = Heatmap(mat, name = "foo") + ha
draw(ht, padding = unit(c(4, 2, 2, 2), "mm"))

plot of chunk unnamed-chunk-17

Adjust positions of column names

In the layout of the heatmap components, column names are put directly below the heatmap body. This will cause problems when annotations are put at the bottom of the heatmap as well:

ha = HeatmapAnnotation(type = df$type,
    col = list(type = c("a" = "red", "b" = "blue")))
Heatmap(mat, bottom_annotation = ha)

plot of chunk unnamed-chunk-18

To solve this problem, we can replace column names with text annotations, which is, we suppress columns when making the heamtap and create a text annotation which is formed by column names.

ha = HeatmapAnnotation(type = df$type, 
    colname = anno_text(colnames(mat), rot = 90, just = "right", offset = unit(1, "npc") - unit(2, "mm")),
    col = list(type = c("a" = "red", "b" = "blue")),
    annotation_height = unit.c(unit(5, "mm"), max_text_width(colnames(mat)) + unit(2, "mm")))
Heatmap(mat, show_column_names = FALSE, bottom_annotation = ha)

plot of chunk unnamed-chunk-19

When add a text annotation, the maximum width of the text should be calculated and set as the height of the text annotation viewport so that all text can be completely shown in the plot. Sometimes, you also need to set rot, just and offset to align the text to the correct anchor positions.

Mark some of the rows/columns

From version 1.8.0, a new annotation function anno_link() was added which connects labels and subset of the rows by links. It is helpful when there are many rows/columns and we want to mark some of the rows (e.g. in a gene expression matrix, we want to mark some important genes of interest.)

mat = matrix(rnorm(10000), nr = 1000)
rownames(mat) = sprintf("%.2f", rowMeans(mat))
subset = sample(1000, 20)
labels = rownames(mat)[subset]
Heatmap(mat, show_row_names = FALSE, show_row_dend = FALSE, show_column_dend = FALSE) + 
rowAnnotation(link = row_anno_link(at = subset, labels = labels),
  width = unit(1, "cm") + max_text_width(labels))

plot of chunk unnamed-chunk-20

# here unit(1, "cm") is width of segments

There are also two shortcut functions: row_anno_link() and column_anno_link().

Session info

sessionInfo()
## R Under development (unstable) (2017-10-20 r73567)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.3 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.7-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.7-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
##  [4] LC_COLLATE=C               LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
## [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] stats4    parallel  grid      stats     graphics  grDevices utils     datasets  methods  
## [10] base     
## 
## other attached packages:
##  [1] dendextend_1.5.2      dendsort_0.3.3        cluster_2.0.6         HilbertCurve_1.9.1   
##  [5] GenomicRanges_1.31.0  GenomeInfoDb_1.15.0   IRanges_2.13.0        S4Vectors_0.17.0     
##  [9] BiocGenerics_0.25.0   circlize_0.4.1        ComplexHeatmap_1.17.1 knitr_1.17           
## [13] markdown_0.8         
## 
## loaded via a namespace (and not attached):
##  [1] fastcluster_1.1.24      shape_1.4.3             modeltools_0.2-21       GetoptLong_0.1.6       
##  [5] kernlab_0.9-25          lattice_0.20-35         colorspace_1.3-2        viridisLite_0.2.0      
##  [9] rlang_0.1.2             prabclus_2.2-6          RColorBrewer_1.1-2      fpc_2.1-10             
## [13] GenomeInfoDbData_0.99.1 plyr_1.8.4              robustbase_0.92-8       stringr_1.2.0          
## [17] zlibbioc_1.25.0         munsell_0.4.3           gtable_0.2.0            GlobalOptions_0.0.12   
## [21] mvtnorm_1.0-6           evaluate_0.10.1         flexmix_2.3-14          class_7.3-14           
## [25] highr_0.6               DEoptimR_1.0-8          trimcluster_0.1-2       Rcpp_0.12.13           
## [29] scales_0.5.0            diptest_0.75-7          XVector_0.19.0          mime_0.5               
## [33] gridExtra_2.3           rjson_0.2.15            ggplot2_2.2.1           png_0.1-7              
## [37] stringi_1.1.5           tools_3.5.0             HilbertVis_1.37.0       bitops_1.0-6           
## [41] magrittr_1.5            RCurl_1.95-4.8          lazyeval_0.2.1          tibble_1.3.4           
## [45] whisker_0.3-2           MASS_7.3-47             viridis_0.4.0           mclust_5.3             
## [49] nnet_7.3-12             compiler_3.5.0