## 1.設(shè)置當前工作目錄
setwd("./ComplexHeatmap")
## 2.安裝和導入R包：ComplexHeatmap
### 2.1 Bioconductor安裝
if (!requireNamespace("BiocManager", quietly = TRUE))
? install.packages("BiocManager")
BiocManager::install("ComplexHeatmap")
### 2.2 導入R包
library(ComplexHeatmap)
library(openxlsx)
## 3.R包簡要信息
### 3.1 Description
# Package: ComplexHeatmap
# Type: Package
# Title: Make Complex Heatmaps
# Version: 2.2.0
# Date: 2019-10-22
# Author: Zuguang Gu
# Maintainer: Zuguang Gu <z.gu@dkfz.de>
#? Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices
# Imports: circlize (>= 0.4.5), GetoptLong, colorspace, clue,
# RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png
# Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg,
# tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2,
# glue, GenomicRanges
# VignetteBuilder: knitr
# Description: Complex heatmaps are efficient to visualize associations
# between different sources of data sets and reveal potential patterns.
# Here the ComplexHeatmap package provides a highly flexible way to arrange
# multiple heatmaps and supports various annotation graphics.
# biocViews: Software, Visualization, Sequencing
# URL: https://github.com/jokergoo/ComplexHeatmap,
# https://jokergoo.github.io/ComplexHeatmap-reference/book/
#? License: MIT + file LICENSE
# git_url: https://git.bioconductor.org/packages/ComplexHeatmap
# git_branch: RELEASE_3_10
# git_last_commit: 8ef3ec8
# git_last_commit_date: 2019-10-29
# Date/Publication: 2019-10-29
# NeedsCompilation: no
# Packaged: 2019-10-30 03:00:31 UTC; biocbuild
# Built: R 3.6.1; ; 2019-10-30 12:58:59 UTC; windows
### 3.2 Main function
ls(package:ComplexHeatmap)
# [1] "%v%"
# [2] "[.AnnotationFunction"
# [3] "[.comb_mat"
# [4] "[.Heatmap"
# [5] "[.HeatmapAnnotation"
# [6] "[.HeatmapList"
# [7] "[.SingleAnnotation"
# [8] "+.AdditiveUnit"
# [9] "add_heatmap"
# [10] "AdditiveUnit"
# [11] "adjust_dend_by_x"
# [12] "adjust_heatmap_list"
# [13] "anno_barplot"
# [14] "anno_block"
# [15] "anno_boxplot"
# [16] "anno_density"
# [17] "anno_empty"
# [18] "anno_histogram"
# [19] "anno_horizon"
# [20] "anno_image"
# [21] "anno_joyplot"
# [22] "anno_lines"
# [23] "anno_link"
# [24] "anno_mark"
# [25] "anno_oncoprint_barplot"
# [26] "anno_points"
# [27] "anno_simple"
# [28] "anno_summary"
# [29] "anno_text"
# [30] "anno_zoom"
# [31] "annotation_axis_grob"
# [32] "annotation_legend_size"
# [33] "AnnotationFunction"
# [34] "c.ColorMapping"
# [35] "c.HeatmapAnnotation"
# [36] "cluster_within_group"
# [37] "color_mapping_legend"
# [38] "ColorMapping"
# [39] "column_dend"
# [40] "column_order"
# [41] "columnAnnotation"
# [42] "comb_degree"
# [43] "comb_name"
# [44] "comb_size"
# [45] "component_height"
# [46] "component_width"
# [47] "copy_all"
# [48] "decorate_annotation"
# [49] "decorate_column_dend"
# [50] "decorate_column_names"
# [51] "decorate_column_title"
# [52] "decorate_dend"
# [53] "decorate_dimnames"
# [54] "decorate_heatmap_body"
# [55] "decorate_row_dend"
# [56] "decorate_row_names"
# [57] "decorate_row_title"
# [58] "decorate_title"
# [59] "default_axis_param"
# [60] "default_get_type"
# [61] "dend_heights"
# [62] "dend_xy"
# [63] "dendrogramGrob"
# [64] "densityHeatmap"
# [65] "dim.Heatmap"
# [66] "dist2"
# [67] "draw"
# [68] "draw_annotation"
# [69] "draw_annotation_legend"
# [70] "draw_dend"
# [71] "draw_dimnames"
# [72] "draw_heatmap_body"
# [73] "draw_heatmap_legend"
# [74] "draw_heatmap_list"
# [75] "draw_title"
# [76] "extract_comb"
# [77] "get_color_mapping_list"
# [78] "get_legend_param_list"
# [79] "getXY_in_parent_vp"
# [80] "grid.annotation_axis"
# [81] "grid.boxplot"
# [82] "grid.dendrogram"
# [83] "grid.draw.Legends"
# [84] "Heatmap"
# [85] "heatmap_legend_size"
# [86] "HeatmapAnnotation"
# [87] "HeatmapList"
# [88] "height.AnnotationFunction"
# [89] "height.Heatmap"
# [90] "height.HeatmapAnnotation"
# [91] "height.HeatmapList"
# [92] "height.Legends"
# [93] "height.SingleAnnotation"
# [94] "height<-.AnnotationFunction"
# [95] "height<-.HeatmapAnnotation"
# [96] "height<-.SingleAnnotation"
# [97] "heightDetails.annotation_axis"
# [98] "heightDetails.legend"
# [99] "heightDetails.legend_body"
# [100] "heightDetails.packed_legends"
# [101] "ht_global_opt"
# [102] "ht_opt"
# [103] "is_abs_unit"
# [104] "Legend"
# [105] "Legends"
# [106] "length.HeatmapAnnotation"
# [107] "length.HeatmapList"
# [108] "list_components"
# [109] "list_to_matrix"
# [110] "make_column_cluster"
# [111] "make_comb_mat"
# [112] "make_layout"
# [113] "make_row_cluster"
# [114] "map_to_colors"
# [115] "max_text_height"
# [116] "max_text_width"
# [117] "merge_dendrogram"
# [118] "names.HeatmapAnnotation"
# [119] "names.HeatmapList"
# [120] "names<-.HeatmapAnnotation"
# [121] "ncol.Heatmap"
# [122] "nobs.AnnotationFunction"
# [123] "nobs.HeatmapAnnotation"
# [124] "nobs.SingleAnnotation"
# [125] "normalize_comb_mat"
# [126] "nrow.Heatmap"
# [127] "oncoPrint"
# [128] "order.comb_mat"
# [129] "packLegend"
# [130] "pindex"
# [131] "prepare"
# [132] "print.comb_mat"
# [133] "re_size"
# [134] "restore_matrix"
# [135] "row_anno_barplot"
# [136] "row_anno_boxplot"
# [137] "row_anno_density"
# [138] "row_anno_histogram"
# [139] "row_anno_link"
# [140] "row_anno_points"
# [141] "row_anno_text"
# [142] "row_dend"
# [143] "row_order"
# [144] "rowAnnotation"
# [145] "set_component_height"
# [146] "set_component_width"
# [147] "set_name"
# [148] "set_size"
# [149] "SingleAnnotation"
# [150] "size.AnnotationFunction"
# [151] "size.HeatmapAnnotation"
# [152] "size.SingleAnnotation"
# [153] "size<-.AnnotationFunction"
# [154] "size<-.HeatmapAnnotation"
# [155] "size<-.SingleAnnotation"
# [156] "smartAlign2"
# [157] "str.comb_mat"
# [158] "subset_gp"
# [159] "subset_matrix_by_row"
# [160] "subset_vector"
# [161] "summary.Heatmap"
# [162] "summary.HeatmapList"
# [163] "t.comb_mat"
# [164] "test_alter_fun"
# [165] "unify_mat_list"
# [166] "UpSet"
# [167] "upset_right_annotation"
# [168] "upset_top_annotation"
# [169] "width.AnnotationFunction"
# [170] "width.Heatmap"
# [171] "width.HeatmapAnnotation"
# [172] "width.HeatmapList"
# [173] "width.Legends"
# [174] "width.SingleAnnotation"
# [175] "width<-.AnnotationFunction"
# [176] "width<-.HeatmapAnnotation"
# [177] "width<-.SingleAnnotation"
# [178] "widthDetails.annotation_axis"
# [179] "widthDetails.legend"
# [180] "widthDetails.legend_body"
# [181] "widthDetails.packed_legends"
## 4.測試
### 4.1 讀取測試數(shù)據(jù)
data <- read.xlsx("Protein_Expression_Data.xlsx",
? ? ? ? ? ? ? ? ? sheet = "data",
? ? ? ? ? ? ? ? ? startRow = 1,
? ? ? ? ? ? ? ? ? colNames = T,
? ? ? ? ? ? ? ? ? rowNames = F,
? ? ? ? ? ? ? ? ? detectDates = F)
dim(data)
# [1] 591? 19
colnames(data)
# [1] "Accession"? ? ? ? ? ? ? ?
# [2] "Gene.Name"? ? ? ? ? ? ? ?
# [3] "Description"? ? ? ? ? ? ?
# [4] "Coverage.[%]"? ? ? ? ? ? ?
# [5] "#.Peptides"? ? ? ? ? ? ? ?
# [6] "#.PSMs"? ? ? ? ? ? ? ? ? ?
# [7] "#.Unique.Peptides"? ? ? ?
# [8] "#.AAs"? ? ? ? ? ? ? ? ? ?
# [9] "MW.[kDa]"? ? ? ? ? ? ? ? ?
# [10] "calc..pI"? ? ? ? ? ? ? ? ?
# [11] "Score.Sequest.HT:.Sequest.HT"
# [12] "C1"? ? ? ? ? ? ? ? ? ? ? ?
# [13] "T2"? ? ? ? ? ? ? ? ? ? ? ?
# [14] "C3"? ? ? ? ? ? ? ? ? ? ? ?
# [15] "T4"? ? ? ? ? ? ? ? ? ? ? ?
# [16] "C5"? ? ? ? ? ? ? ? ? ? ? ?
# [17] "T6"? ? ? ? ? ? ? ? ? ? ? ?
# [18] "C7"? ? ? ? ? ? ? ? ? ? ? ?
# [19] "T8"
#@ 提取所需要的列
data_clean <- data[,12:19]
dim(data_clean)
# [1] 591? 8
#@ 合并新的蛋白表達矩陣數(shù)據(jù)
data_clean_new <- data.frame(data$Accession, data_clean)
#@ 修改列名
colnames(data_clean_new)[1] <- "Accession"
#@ 查看前六行數(shù)據(jù)
head(data_clean_new)
# Accession? ? C1? T2? ? C3? ? T4? ? C5? ? T6? ? C7? ? T8
# 1? ? P04114 105.2 93.8 125.2 139.6? 82.8? 76.9? 74.2 102.2
# 2? ? P0C0L5? 68.9 74.7 121.7 122.0? 85.3? 98.4 114.2 114.8
# 3? ? P0C0L4? 88.4 95.4 111.9 133.2? 81.3 101.6 103.9? 84.3
# 4? ? P02768? 90.9 84.0 110.1? 89.3 120.8 100.5 101.1 103.2
# 5? ? P01024? 89.5 83.9 105.0? 94.8? 97.6? 70.5 121.2 137.5
# 6? ? P00734? 93.2 92.9 101.1 130.4? 76.5 110.0 107.9? 88.1
rownames(data_clean_new) <- data_clean_new$Accession
data_clean_new$Accession <- NULL
right_annotation <- colMeans(data_clean_new)
class(right_annotation)
# [1] "numeric"
data_clean_new <- as.matrix(data_clean_new)
##********************************************************##
### 4.2 繪制barplot_heatmap ###
#### 4.2.1 colMean
ha = HeatmapAnnotation(barplot = anno_barplot(right_annotation, height = unit(3, "cm"),
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? box_width = 0.9, outline = FALSE, gp = gpar(fill = 1:8)))
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? top_annotation = ha,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16))
?
#### 4.2.2 colSum
right_annotation <- colSums(data_clean_new)
ha = HeatmapAnnotation(barplot = anno_barplot(right_annotation, height = unit(3, "cm"),
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? box_width = 0.9, outline = FALSE, gp = gpar(fill = 1:8)))
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? top_annotation = ha,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16))
?
### 4.3 boxplot_heatmap ###
#### 4.3.1 default color
ha = HeatmapAnnotation(boxplot = anno_boxplot(data_clean_new, height = unit(3, "cm"), box_width = 0.9, outline = FALSE))
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? top_annotation = ha,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16))
?
#### 4.3.2 custom color
ha = HeatmapAnnotation(boxplot = anno_boxplot(data_clean_new, height = unit(3, "cm"), box_width = 0.9, outline = FALSE, gp = gpar(fill = 1:8)))
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? top_annotation = ha,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16))
?
### 4.4 Block annotation Heatmap ###
#### 4.4.1 top_annotation
ha <- HeatmapAnnotation(block = anno_block(gp = gpar(2:4),
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? labels = c("sample1", "sample2", "sample3"), labels_gp = gpar(col = c("green", "blue", "orange"))))
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? top_annotation = ha,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16),
? ? ? ? column_km = 3)
?
#### 4.4.2 left_annotation
ha <- rowAnnotation(block = anno_block(gp = gpar(2:4),
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? labels = c("group1", "group2", "group3", "group4", "group5"), labels_gp = gpar(col = c("green", "blue", "orange", "red", "purple"))))
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? left_annotation = ha,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16),
? ? ? ? row_km = 5)
?
#### 4.4.3 Combine top and left annotation
top_annotation <- HeatmapAnnotation(block = anno_block(gp = gpar(2:4),
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? labels = c("sample1", "sample2", "sample3"), labels_gp = gpar(col = c("green", "blue", "orange"))))
left_annotation <- rowAnnotation(block = anno_block(gp = gpar(2:4),
? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? labels = c("group1", "group2", "group3", "group4", "group5"), labels_gp = gpar(col = c("green", "blue", "orange", "red", "purple"))))
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? top_annotation = top_annotation,
? ? ? ? left_annotation = left_annotation,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16),
? ? ? ? column_km = 3,
? ? ? ? row_km = 5)
?
### 4.5 anno_density
ha <- HeatmapAnnotation(density = anno_density(data_clean_new, gp = gpar(fill = 1:8)))
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? top_annotation = ha,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16))
?
### 4.6 histogram annotation
ha <- HeatmapAnnotation(histogram = anno_histogram(data_clean_new, gp = gpar(fill = 1:8)))
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? top_annotation = ha,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16))
?
### 4.7 joyplot annotation
ha <- HeatmapAnnotation(joyplot = anno_joyplot(data_clean_new, gp = gpar(fill = 1:8)))
draw(ha, test = "joyplot")
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? top_annotation = ha,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16))
?
### 4.8 lines annotation
ha <- rowAnnotation(lines = anno_lines(data_clean_new, add_points = TRUE, pt_gp = gpar(col = 5:6), pch = c(1, 16)))
draw(ha, test = "lines")
Heatmap(data_clean_new,
? ? ? ? name = "protein exp",
? ? ? ? left_annotation = ha,
? ? ? ? na_col = "grey",
? ? ? ? row_names_gp = gpar(fontsize = 0.5),
? ? ? ? column_names_gp = gpar(fontsize = 16))
?
## 5.結(jié)束
sessionInfo()
# R version 3.6.3 (2020-02-29)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 18363)
#
# 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
# [7] methods? base?
#
# other attached packages:
#? [1] openxlsx_4.1.4? ? ? ComplexHeatmap_2.2.0
#
# loaded via a namespace (and not attached):
#? [1] Rcpp_1.0.4? ? ? ? ? rstudioapi_0.11? ? cluster_2.1.0? ?
# [4] hms_0.5.3? ? ? ? ? progress_1.2.2? ? ? colorspace_1.4-1
# [7] clue_0.3-57? ? ? ? rjson_0.2.20? ? ? ? R6_2.4.1? ? ? ?
# [10] rlang_0.4.5? ? ? ? tools_3.6.3? ? ? ? parallel_3.6.3?
# [13] circlize_0.4.8? ? ? png_0.1-7? ? ? ? ? crayon_1.3.4? ?
# [16] zip_2.0.4? ? ? ? ? BiocManager_1.30.10 RColorBrewer_1.1-2
# [19] vctrs_0.2.4? ? ? ? GlobalOptions_0.1.1 shape_1.4.4? ? ?
# [22] stringi_1.4.6? ? ? compiler_3.6.3? ? ? prettyunits_1.1.1
# [25] pkgconfig_2.0.3? ? GetoptLong_0.1.8
