修改参数绘制不一样的热图_2020-02-15

## 1.设置当前工作目录

setwd("./pheatmap/")

## 2.导入R包

library(pheatmap)

## 3.增加参数，绘制不一样的热图

### 3.1 pheatmap函数的结构

str(pheatmap)
function (mat, color = colorRampPalette(rev(brewer.pal(n = 7, 
                                                       name = "RdYlBu")))(100), kmeans_k = NA, breaks = NA, 
          border_color = "grey60", cellwidth = NA, cellheight = NA, 
          scale = "none", cluster_rows = TRUE, cluster_cols = TRUE, 
          clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean", 
          clustering_method = "complete", clustering_callback = identity2, 
          cutree_rows = NA, cutree_cols = NA, treeheight_row = ifelse((class(cluster_rows) == 
                                                                         "hclust") || cluster_rows, 50, 0), treeheight_col = ifelse((class(cluster_cols) == 
                                                                                                                                       "hclust") || cluster_cols, 50, 0), legend = TRUE, 
          legend_breaks = NA, legend_labels = NA, annotation_row = NA, 
          annotation_col = NA, annotation = NA, annotation_colors = NA, 
          annotation_legend = TRUE, annotation_names_row = TRUE, 
          annotation_names_col = TRUE, drop_levels = TRUE, show_rownames = T, 
          show_colnames = T, main = NA, fontsize = 10, fontsize_row = fontsize, 
          fontsize_col = fontsize, angle_col = c("270", "0", 
                                                 "45", "90", "315"), display_numbers = F, number_format = "%.2f", 
          number_color = "grey30", fontsize_number = 0.8 * fontsize, 
          gaps_row = NULL, gaps_col = NULL, labels_row = NULL, 
          labels_col = NULL, filename = NA, width = NA, height = NA, 
          silent = FALSE, na_col = "#DDDDDD", ...)

#@ 可以说虽然pheatmap包只有一个函数，但是其参数却很多。

### 3.2 构建数据矩阵

# Create test matrix
test = matrix(rnorm(200), 20, 10)
test[1:10, seq(1, 10, 2)] = test[1:10, seq(1, 10, 2)] + 3
test[11:20, seq(2, 10, 2)] = test[11:20, seq(2, 10, 2)] + 2
test[15:20, seq(2, 10, 2)] = test[15:20, seq(2, 10, 2)] + 4
colnames(test) = paste("Sample", 1:10, sep = "")
rownames(test) = paste("Gene", 1:20, sep = "")

test # 查看test所有行/列内容
#              Sample1    Sample2     Sample3    Sample4      Sample5     Sample6     Sample7    Sample8    Sample9    Sample10
# Gene1   3.7957568965  1.8233967  4.90560319  0.4067799  1.744039844 -0.02343351  3.48676035 -1.2406482  4.5505502  1.76937939
# Gene2   3.6552355276 -1.1993517  2.84112928 -0.3302270  2.491619748 -1.38009883  3.39422605  1.5526861  2.6797210  0.34295123
# Gene3   3.0609460815  0.3939751  4.90184120 -1.2154164  2.785525236  2.10026720  2.14067630  0.8166145  1.7517652  0.01996091
# Gene4   1.8684783946 -0.5386937  4.04685597  0.5901531  5.557510665 -0.19432126  3.31743363 -2.5144840  5.2018033 -0.04044510
# Gene5   2.0102636582 -0.9290359  2.40038679 -0.7775586  4.544655968 -1.19577000  3.84144210 -0.8475016  4.0338375 -0.54380074
# Gene6   3.0913495948  1.1772101  2.55722993 -0.6539475  2.549411967 -2.17690077  4.31288259  1.9227596  2.9604031 -0.03828152
# Gene7   3.8568183324 -0.4995627  3.57153508  0.5986590  3.122804423  1.37560199  2.43122407 -0.7429620  2.0837279  0.32902492
# Gene8   2.4509152396 -0.9611449  3.71700755  2.5553465  5.737982513  0.95604710  4.76721774 -1.2094103  2.2500003  0.35622822
# Gene9   1.6912999340 -0.2795518  4.00216213 -0.7162299  3.454144641  1.52470003  1.69047393 -1.5661280  4.0190400  0.63367912
# Gene10  0.6252480813  0.7438685  2.79662365  0.1703116  4.027609805  1.48381433  1.33705747  0.7747472  1.6031794  0.84923383
# Gene11 -0.4415825011  1.6080083 -0.19851846  2.7917330 -0.272474105 -0.10548920 -1.16025639  4.8305640  1.5770095  2.37149165
# Gene12 -0.6486606194  2.3700840 -0.77680084  1.4526694 -0.690304011  2.72308752  0.56949307  2.0399642 -0.3389819  1.40462561
# Gene13  0.0003821621  2.7113877 -0.39020907  2.8151354 -0.143181040  2.95203997 -0.85860110  2.4843515  0.9566911  2.39021211
# Gene14 -0.8011450013  4.0355510 -0.13017966  1.9029852  0.545175405  2.56665354  0.64394177  0.7000872  1.2690745  0.81502417
# Gene15 -0.5260242769  5.1100108  0.64137183  5.6425943  0.795887942  6.16224530 -0.40601303  5.8162889  0.1890412  6.15425580
# Gene16  1.1517317679  4.8100645 -0.33636956  5.2866118  0.265741749  5.11349791 -0.08855405  4.9829329 -0.8593587  7.52634773
# Gene17 -0.3555386628  6.8908341 -0.08050773  5.6959011  0.294486045  5.95486324  0.03772128  7.3472300 -1.2174207  5.96422351
# Gene18  0.5116797595  7.1544451 -0.18289447  5.2302485 -0.332464869  6.63425428 -0.54265890  5.0684743  0.7049639  7.32387247
# Gene19  1.7883182624  7.0628887 -0.43384416  4.0698986  0.003087234  5.41186588 -0.79840591  6.1149826  1.4828378  6.18828734
# Gene20 -0.5365331816  6.5070019 -1.49916738  6.3740146  0.775502704  6.29618602 -0.83917708  4.4833950  1.5096281  7.02968546

### 3.3 绘制热图

 

# Draw heatmaps
pheatmap(test) # 默认参数绘制热图

 

pheatmap(test, kmeans_k = 2) # 对基因进行kmeans = 2聚类

 

pheatmap(test, kmeans_k = 3) # kmeans = 3聚类

 

pheatmap(test, scale = "row", clustering_distance_rows = "correlation") # scale = "row"，按行进行缩放，还可以按列column缩放；clustering_distance_rows = "correlation"，对行进行Pearson相关性距离进行聚类，也可以按照euclidean进行聚类

pheatmap(test, color = colorRampPalette(c("navy", "white", "firebrick3"))(50)) # 修改默认颜色，重新绘制热图

## 4.结束

 

sessionInfo()
# R version 3.6.2 (2019-12-12)
# 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] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] pheatmap_1.0.12
# 
# loaded via a namespace (and not attached):
# [1] colorspace_1.4-1   scales_1.1.0       compiler_3.6.2     R6_2.4.1          
# [5] tools_3.6.2        gtable_0.3.0       RColorBrewer_1.1-2 grid_3.6.2        
# [9] lifecycle_0.1.0    packrat_0.5.0      munsell_0.5.0      rlang_0.4.4