Lesson 08 for Plotting in R for Biologists

最新推荐文章于 2024-04-26 09:46:10 发布

R语言中文社区

最新推荐文章于 2024-04-26 09:46:10 发布

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本文链接：https://blog.csdn.net/kMD8d5R/article/details/81073844

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作者简介

taoyan：R语言中文社区特约作家，伪码农，R语言爱好者，爱开源。

个人博客: https://ytlogos.github.io/

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这节课是最后一节课，主要将如何绘制热图(heatmap)。实际上关于热图的绘制，我以前写了一篇博客：R语言学习笔记之热图绘制，里面写的十分详细。但是今天热图绘制主要利用一个新的R包ComplexHeatmap进行绘制。

包安装

source("https://bioconductor.org/biocLite.R")

options(BioC_mirror="http://mirrors.ustc.edu.cn/bioc/")

biocLite("ComplexHeatmap")

数据加载

library(ComplexHeatmap)

my_data <- read.table("copy_number_data.txt", sep = "\t", quote="", stringsAsFactors = FALSE, header = TRUE)

head(my_data[,1:6])

## CHR START END X.SRR089523. X.SRR089526. X.SRR089529.

## 1 chr1 53440429 53494914 1.1002112 1.1000844 1.0487301

## 2 chr1 105459037 105514187 1.1860780 0.6553897 0.4980016

## 3 chr1 183998520 184048557 1.3791250 1.2024487 0.5735184

## 4 chr1 236135655 236186012 0.8987158 1.1182392 0.6396842

## 5 chr2 38944803 38996507 1.0788216 0.9663390 1.0473623

## 6 chr2 97248366 97298651 1.0459629 1.0658991 1.0473623

#绘制热图前先进行矩阵化

my_matrix <- as.matrix(my_data[, c(4:100)])

head(my_matrix[,1:4])

## X.SRR089523. X.SRR089526. X.SRR089529. X.SRR089533.

## [1,] 1.1002112 1.1000844 1.0487301 0.5656784

## [2,] 1.1860780 0.6553897 0.4980016 0.5656784

## [3,] 1.3791250 1.2024487 0.5735184 1.0362551

## [4,] 0.8987158 1.1182392 0.6396842 0.4659238

## [5,] 1.0788216 0.9663390 1.0473623 1.1702930

## [6,] 1.0459629 1.0658991 1.0473623 1.2298119

#将染色体信息存储好以便后续热图注释

chromosome_info <- data.frame(chrom=my_data$CHR)

可视化

Heatmap(my_matrix)

640?wx_fmt=jpeg 可以看到使用默认参数热图时十分不美观，可以进行部分调整

#坐标旋转

my_matrix <- t(my_matrix)

Heatmap(my_matrix)

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坐标标签还是十分乱，还得进行调整

Heatmap(my_matrix, cluster_columns = FALSE)#列不聚类

将坐标标签位置置于左边

Heatmap(my_matrix,

cluster_columns = FALSE,

row_names_side = "left",

row_hclust_side = "left",

row_names_gp = gpar(cex=0.6)

)

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Heatmap(my_matrix,

cluster_columns = FALSE,

row_names_side = "left",

row_hclust_side = "left",

row_names_gp = gpar(cex=0.6),

row_hclust_width = unit(3, "cm"))

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热图绘制的时候可以使用不同的距离计算方式以及聚类方法，具体的用法可以参考我以前的文章：R语言学习笔记之热图绘制。

Heatmap(my_matrix,

cluster_columns = FALSE,

row_names_side = "left",

row_hclust_side = "left",

row_names_gp = gpar(cex=0.6),

row_hclust_width = unit(3, "cm"),

clustering_distance_rows = "maximum",

clustering_method_rows = "ward.D")

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热图注释

主要是对聚成的类进行颜色标记

library(dendextend)

dend <- hclust(dist(my_matrix, method = "maximum"), method = "ward.D")

Heatmap(my_matrix,

cluster_columns = FALSE,

row_names_side = "left",

row_hclust_side = "left",

row_names_gp = gpar(cex=0.6),

row_hclust_width = unit(3, "cm"),

cluster_rows = color_branches(dend, k=3))

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将热图分类

随便你先分成几类，但是一般来说有一个最佳分类数，可参考我的另一篇博客：R语言学习笔记之聚类分析

Heatmap(my_matrix,

cluster_columns = FALSE,

row_names_side = "left",

row_hclust_side = "left",

row_names_gp = gpar(cex=0.6),

row_hclust_width = unit(3, "cm"),

clustering_distance_rows = "maximum",

clustering_method_rows = "ward.D",

km=2)

根据染色体信息进行注释

chromosome_colors <- c(rep(c("black","white"),11), "red")

names(chromosome_colors) <- paste("chr",c(seq(1:22), "X"), sep = "")

Heatmap(my_matrix,

cluster_columns = FALSE,

row_names_side = "left",

row_hclust_side = "left",

row_names_gp = gpar(cex=0.6),

row_hclust_width = unit(3, "cm"),

clustering_distance_rows = "maximum",

clustering_method_rows = "ward.D",

km=2,

bottom_annotation = HeatmapAnnotation(chromosome_info, col = list(chrom=chromosome_colors), show_legend = FALSE))

640?wx_fmt=jpeg SessionInfo

sessionInfo()

## R version 3.4.3 (2017-11-30)

## Platform: x86_64-w64-mingw32/x64 (64-bit)

## Running under: Windows 10 x64 (build 16299)

##

## Matrix products: default

##

## locale:

## [1] LC_COLLATE=Chinese (Simplified)_China.936

## [2] LC_CTYPE=Chinese (Simplified)_China.936

## [3] LC_MONETARY=Chinese (Simplified)_China.936

## [4] LC_NUMERIC=C

## [5] LC_TIME=Chinese (Simplified)_China.936

##

## attached base packages:

## [1] grid stats graphics grDevices utils datasets methods

## [8] base

##

## other attached packages:

## [1] dendextend_1.6.0 ComplexHeatmap_1.17.1

##

## loaded via a namespace (and not attached):

## [1] Rcpp_0.12.15 DEoptimR_1.0-8 compiler_3.4.3

## [4] pillar_1.1.0 RColorBrewer_1.1-2 plyr_1.8.4

## [7] viridis_0.4.1 class_7.3-14 prabclus_2.2-6

## [10] tools_3.4.3 digest_0.6.15 mclust_5.4

## [13] viridisLite_0.3.0 evaluate_0.10.1 tibble_1.4.2

## [16] gtable_0.2.0 lattice_0.20-35 rlang_0.1.6

## [19] yaml_2.1.16 mvtnorm_1.0-7 gridExtra_2.3

## [22] trimcluster_0.1-2 stringr_1.2.0 knitr_1.19

## [25] cluster_2.0.6 GlobalOptions_0.0.12 fpc_2.1-11

## [28] diptest_0.75-7 nnet_7.3-12 stats4_3.4.3

## [31] rprojroot_1.3-2 robustbase_0.92-8 GetoptLong_0.1.6

## [34] flexmix_2.3-14 rmarkdown_1.8 kernlab_0.9-25

## [37] ggplot2_2.2.1.9000 magrittr_1.5 whisker_0.3-2

## [40] modeltools_0.2-21 backports_1.1.2 scales_0.5.0.9000

## [43] htmltools_0.3.6 MASS_7.3-48 shape_1.4.3

## [46] circlize_0.4.3 colorspace_1.3-2 stringi_1.1.6

## [49] lazyeval_0.2.1 munsell_0.4.3 rjson_0.2.15

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创建属于自己的调色板

Lesson 01 for Plotting in R for Biologists

Lesson 02&03 for Plotting in R for Biologists

Lesson 04 for Plotting in R for Biologists

Lesson 05 for Plotting in R for Biologists

Lesson 06 for Plotting in R for Biologists

Lesson 07 for Plotting in R for Biologists

R语言学习笔记之热图绘制

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