作者：Zuguang Gu8
    翻译：Steven Shen
    原文：https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html

    The main feature of ComplexHeatmap package is it supports to concatenate a list of heatmaps and annotations horizontally or vertically so that it makes it possible to visualize the associations from various sources of information. In this chapter, we mainly introduce the horizontal concatenation because this is the major case we will use in the analysis. In the end we show some examples of vertical concatenation. The concept behind for horizontal and vertical concatenation basically is similar.

    For the horizontal concatenation, the number of rows for all heatmaps and annotations should be the same. In following we first introduce the concatenation of heatmaps and later we will show how to concatenate heatmaps with annotations.

    In following example, there are three matrices where the third heatmap is a vector and it will be transformed as a one-column matrix. The one-column heatmap is sometimes useful when you concatenate a list of heatmaps that it can show e.g. annotations for each row or some scores of each row. E.g. if rows are genes, the type of the genes (i.e. protein coding or not) can be represented as a one-column character matrix, and the p-value or the fold change from differential expression analysis can be represented as a one-column numeric matrix, and be concatenated to the main expression heatmap.

    1. set.seed(123)
    2. mat1 = matrix(rnorm(80, 2), 8, 10)
    3. mat1 = rbind(mat1, matrix(rnorm(40, -2), 4, 10))
    4. rownames(mat1) = paste0("R", 1:12)
    5. colnames(mat1) = paste0("C", 1:10)
    7. mat2 = matrix(runif(60, max = 3, min = 1), 6, 10)
    8. mat2 = rbind(mat2, matrix(runif(60, max = 2, min = 0), 6, 10))
    9. rownames(mat2) = paste0("R", 1:12)
    10. colnames(mat2) = paste0("C", 1:10)
    12. le = sample(letters[1:3], 12, replace = TRUE)
    13. names(le) = paste0("R", 1:12)
    15. ind = sample(12, 12)
    16. mat1 = mat1[ind, ]
    17. mat2 = mat2[ind, ]
    18. le = le[ind]

    To concatenate heatmaps, simply use + operator.

    1. ht1 = Heatmap(mat1, name = "rnorm")
    2. ht2 = Heatmap(mat2, name = "runif")
    3. ht3 = Heatmap(le, name = "letters")
    5. ht1 + ht2 + ht3

    4. 热图列表 - 图1

    Under default mode, dendrograms from the second heatmap will be removed and row orders will be the same as the first one. Also row names for the first two heatmaps are removed as well.

    The returned value of the concatenation is a HeatmapList object. Similar as explained in Section 2.11, directly printing ht_list will call draw() method with default settings. With explicitly calling draw() method, you can have more controls on the heatmap list.

    1. ht_list = ht1 + ht2 + ht3
    2. class(ht_list)
    5. ## [1] "HeatmapList"
    6. ## attr(,"package")
    7. ## [1] "ComplexHeatmap"

    You can append any number of heatmaps to the heatmap list. Also you can append a heatmap list to a heatmap list.

    1. # code only for demonstration
    2. ht1 + ht_list
    3. ht_list + ht1
    4. ht_list + ht_list

    NULL can be added to the heatmap list. It would be convinient when users want to construct a heatmap list through a for loop.

    1. # code only for demonstration
    2. ht_list = NULL  ## Heatmap(...) + NULL gives you a HeatmapList object
    3. for(s in sth) {
    4.     ht_list = ht_list + Heatmap(...)
    5. }

    You can also add heatmap annotations to the heatmap list, see more details in Section 4.7.