complexheatmap学习3——热图拼接
2019-07-03 本文已影响58人
drlee_fc74
本文是对于ComplexHeatmap作者说明的学习笔记。如果想看原文可去：https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html
complexheatmap的主要特点是可以组合多个热图成为一个图片。需要注意的是，对于不同热图组合的时候。如果是水平组合，那么不同热图之间的行数必须相同。如果是垂直组合那么不同热图之间的列数必须相同。
我们主要接受的是水平组合。但是垂直组合也是一样的。
最基本的例子
一般来说，不同的热图可以通过+来进行组合。例如下图
library(ComplexHeatmap)
## Loading required package: grid
## ========================================
## ComplexHeatmap version 2.0.0
## Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
## Github page: https://github.com/jokergoo/ComplexHeatmap
## Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
##
## If you use it in published research, please cite:
## Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
## genomic data. Bioinformatics 2016.
## ========================================
library(circlize)
## ========================================
## circlize version 0.4.6
## CRAN page: https://cran.r-project.org/package=circlize
## Github page: https://github.com/jokergoo/circlize
## Documentation: http://jokergoo.github.io/circlize_book/book/
##
## If you use it in published research, please cite:
## Gu, Z. circlize implements and enhances circular visualization
## in R. Bioinformatics 2014.
## ========================================
set.seed(123)
mat1 = matrix(rnorm(80, 2), 8, 10)
mat1 = rbind(mat1, matrix(rnorm(40, -2), 4, 10))
rownames(mat1) = paste0("R", 1:12)
colnames(mat1) = paste0("C", 1:10)
mat2 = matrix(runif(60, max = 3, min = 1), 6, 10)
mat2 = rbind(mat2, matrix(runif(60, max = 2, min = 0), 6, 10))
rownames(mat2) = paste0("R", 1:12)
colnames(mat2) = paste0("C", 1:10)
le = sample(letters[1:3], 12, replace = TRUE)
names(le) = paste0("R", 1:12)
ind = sample(12, 12)
mat1 = mat1[ind, ]
mat2 = mat2[ind, ]
le = le[ind]
ht1 = Heatmap(mat1, name = "rnorm")
ht2 = Heatmap(mat2, name = "runif")
ht3 = Heatmap(le, name = "letters")
ht1 + ht2 + ht3
heatma
标题
我们可以在draw里面的column_title以及row_title来设置标题。同时可以通过row/column_title_gp来自定义变化
col_rnorm = colorRamp2(c(-3, 0, 3), c("green", "white", "red"))
col_runif = colorRamp2(c(0, 3), c("white", "orange"))
col_letters = c("a" = "pink", "b" = "purple", "c" = "blue")
ht1 = Heatmap(mat1, name = "rnorm", col = col_rnorm,
row_title = "Heatmap 1", column_title = "Heatmap 1")
ht2 = Heatmap(mat2, name = "runif", col = col_runif,
row_title = "Heatmap 2", column_title = "Heatmap 2")
ht3 = Heatmap(le, name = "letters", col = col_letters)
ht_list = ht1 + ht2 + ht3
draw(ht_list, row_title = "Three heatmaps, row title", row_title_gp = gpar(col = "red"),
column_title = "Three heatmaps, column title", column_title_gp = gpar(fontsize = 16))
image.png
热图的大小
热图的大小，我们可以在制作某一个热图的时候，自己先设置好。然后连接到一起就行
ht2 = Heatmap(mat2, name = "runif", col = col_runif, width = unit(4, "cm"))
ht3 = Heatmap(le, name = "letters", col = col_letters, width = unit(5, "mm"))
ht1 + ht2 + ht3
image.png
热图之间的空隙
我们可以通过ht_gap来设置热图的大小。
ht1 = Heatmap(mat1, name = "rnorm", col = col_rnorm)
ht2 = Heatmap(mat2, name = "runif", col = col_runif)
ht3 = Heatmap(le, name = "letters", col = col_letters)
ht_list = ht1 + ht2 + ht3
draw(ht_list, ht_gap = unit(c(3, 10), "mm"))
image.png
基于主要的热图自动调整
在一系列热图当中。永远有一个主要的热图。其他的热图都会基于这个热图来进行自动的调整。主要调整包括： - 其他的热图不会进行行的聚类，同时其他的热图的行的顺序都会和主要热图一致。 - 行名只会包括一个 - 如果主要热图基于行进行分割了，那么其他热图也会进行分割 - 其他热图的高度会和主要热图的高度一致 - 默认的第一个热图会主要热图。但是可以通过main_heatmap来调整。这个参数接受的是热图的名字 - 默认的聚类树和聚类名称是在左侧的。我们可以通过row_dend_side以及row_sub_title_side来进行调整。 - 如果不想进行行的聚类。把第一个聚类设置为否即可。 - 我们可以通过auto_adjust来设置是否打开自动调整。如果不打开。那么就都会显示列名
ht_list = ht2 + ht1 + ht3
draw(ht_list, main_heatmap = "rnorm", row_dend_side = "right", row_sub_title_side = "left")
image.png
draw(ht_list, auto_adjust = FALSE)
image.png
主要热图的设置
一般主要热图可以在Heatmap当中设置好再进行链接的。同时的话，也可以通过draw函数来设置主要热图的。这个设置的主要参数包括 cluster_rows; clustering_distance_rows; clustering_method_rows; row_dend_width; show_row_dend; row_dend_reorder; row_dend_gap; row_order; row_gap; row_km; row_km_repeats; row_split; height; height_heatmap
ht1 = Heatmap(mat1, name = "rnorm", col = col_rnorm, row_km = 2, cluster_rows = FALSE)
ht2 = Heatmap(mat2, name = "runif", col = col_runif)
ht3 = Heatmap(le, name = "letters", col = col_letters)
ht_list = ht1 + ht2 + ht3
draw(ht_list, row_km = 1, row_split = le, cluster_rows = TRUE)
image.png
注释部分的调整
一般来说如果多个热图都有注释的话，那么就会基于主要热图来自动调整。
ha1 = HeatmapAnnotation(foo1 = 1:10, annotation_name_side = "left")
ha2 = HeatmapAnnotation(bar2 = anno_barplot(1:10, height = unit(2, "cm")))
ht1 = Heatmap(mat1, name = "rnorm", col = col_rnorm, top_annotation = ha1)
ht2 = Heatmap(mat2, name = "runif", col = col_runif, top_annotation = ha2)
ht3 = Heatmap(le, name = "letters", col = col_letters)
ht_list = ht1 + ht2 + ht3
draw(ht_list, ht_gap = unit(c(6, 2), "mm"))
image.png
热图和注释联系在一起
+不仅可以用于热图之间的联系，也可以用于热图和注释的联系。
ha1 = rowAnnotation(foo = 1:12, bar = anno_barplot(1:12, width = unit(4, "cm")))
ht1 = Heatmap(mat1, name = "rnorm", col = col_rnorm, row_km = 2)
ht1 + ha1
image.png
基本上热图和行的注释可以通过+来任意的组合
rowAnnotation(foo = 1:12) +
Heatmap(mat1, name = "rnorm", col = col_rnorm, row_km = 2) +
rowAnnotation(bar = anno_barplot(1:12, width = unit(4, "cm"))) +
Heatmap(mat2, name = "runif", col = col_runif)
image.png
注释之间的联系
如果热图和注释可以连接的话，那么注释和注释肯定也可以连接的
rowAnnotation(foo = 1:12) +
rowAnnotation(bar = anno_barplot(1:12, width = unit(4, "cm")))
image.png
垂直的连接
上述讲到的连接都是水平的连接。这样的连接我们使用的是+；如果是垂直的连接的话，那就需要使用%v%号了。其他的设置其实和行一致的
mat1t = t(mat1)
mat2t = t(mat2)
ht1 = Heatmap(mat1t, name = "rnorm", col = col_rnorm, row_km = 2,
left_annotation = rowAnnotation(foo1 = 1:10, bar1 = anno_barplot(1:10)))
ha = HeatmapAnnotation(foo = anno_barplot(1:12, height = unit(2, "cm"),
axis_param = list(side = "right")))
ht2 = Heatmap(mat2t, name = "runif", col = col_runif, row_km = 2,
left_annotation = rowAnnotation(foo2 = 1:10))
ht3 = Heatmap(rbind(letters = le), name = "letters", col = col_letters)
ht_list = ht1 %v% ha %v% ht2 %v% ht3
draw(ht_list, column_km = 2)
image.png
自动调整热图的参数
当我们绘制多个热图的时候。有一些固定的设置想要进行同时的配置。这样的话，我们就可以通过ht_opt参数进行整体配置。其可以进行配置的参数可以参见主页。
ht_opt(heatmap_column_names_gp = gpar(fontface = "italic"),
heatmap_column_title_gp = gpar(fontsize = 10),
legend_border = "black",
heatmap_border = TRUE,
annotation_border = TRUE
)
ht1 = Heatmap(mat1, name = "ht1", column_title = "Heatmap 1",
top_annotation = HeatmapAnnotation(foo = 1:10))
ht2 = Heatmap(mat2, name = "ht2", column_title = "Heatmap 2",
top_annotation = HeatmapAnnotation(bar = 1:10))
ht1 + ht2
image.png
