【零基础学绘图】之气泡图绘制（六）

生信团上海天昊生物

气泡图是R语音中的基础绘图，可用于展示三个变量之间的关系的图表，将一个变量放在x轴，另一个变量放在y轴，而第三个变量则用气泡的大小来表示。通常用于展示差异基因的表达情况、转录因子的分析、物种丰度数据的可视化、富集分析展示等。这里我们介绍2种绘制气泡图的方法：ggpubr绘制气泡图和 ggplot 绘制气泡图。

一

ggpubr绘制气泡图

1. 加载ggpubr包

In [1]:

library(ggpubr)

2. 数据读取

由于表头是数字，需要添加参数check.names = F

In [2]:

df = read.table('phylum_taxon_abundance.xls',header = T,row.names = 1,check.names = F)
head(df)

Out[2]:

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

Proteobacteria 126573 92545 83038 75739 103697 116154 73868 76555 47648 61165 90984 86653 111958 95141 92972 102300

							Actinobacteria

12759 10186 50860 32437 34212 21024 64078 52398 46109 38587 46147 46310 46780 50249 32803 29345
Bacteroidetes 18428 25557 16559 22848 7046 23059 4974 8066 4984 15941 14064 12966 10931 5047 14100 27364
Acidobacteria 16566 26529 6636 16079 7563 10637 8352 11404 11755 7008 8292 9372 6405 5773 10853 6738
Chloroflexi 6665 11038 12520 20040 22476 4146 23314 26628 32961 30103 14238 11799 9819 15672 7421 6116

Firmicutes  6033  13830  21344  3293  18031  10253  12822  5480  35773  6208  13005  20341  7953  21295  19200  12794

3. 气泡图绘制

3.1 绘制不带参数的气泡图

In [3]:

ggballoonplot(df)

Out[3]:

3.2 添加和填充颜色

In [4]:

ggballoonplot(df, color = "red", fill = "blue")

Out[4]:

3.3 按照值的大小填充颜色，并制定气泡图形状

In [5]:

ggballoonplot(df, fill = "value", shape =21 ,) + gradient_fill(c("blue", "white", "red"))

Out[5]:

3.4 填充数值

show.label =F 默认不填充数值， show.label =T 填充数值
选择size参数固定图形大小

In [6]:

ggballoonplot(df, fill = "value", color = "lightgray",size = 3, show.label =F)+ gradient_fill(c("blue", "white", "red"))

Out[6]:

二

ggplot2绘制气泡图

1. 加载ggplot2包

In [7]:

library(ggplot2)

2. 数据预处理

stack是堆栈的意思，默认按列堆数据
In [8]:

data = stack(df)
colnames(data) = c('Abundance','sample')
head(data)

Out[8]:

Abundance sample
126573 1
12759 1
18428 1
16566 1
6665 1
6033 1

In [9]:

data$phylum = rep(rownames(df), times = ncol(df))
head(data)

Out[9]:

Abundance sample phylum
126573 1 Proteobacteria
12759 1 Actinobacteria
18428 1 Bacteroidetes
16566 1 Acidobacteria
6665 1 Chloroflexi
6033 1 Firmicutes

添加分组信息，本次分析将16个样品分为2组，组名分别未A、B

In [10]:

colnames(df)

Out[10]:

'1' '2' '3' '4' '5' '6' '7' '8' '9' '10' '11' '12' '13' '14' '15' '16'

In [11]:

length(colnames(df))

Out[11]:

16

In [12]:

rownames(df)

Out[12]:

'Proteobacteria' 'Actinobacteria' 'Bacteroidetes' 'Acidobacteria' 'Chloroflexi' 'Firmicutes' 'Verrucomicrobia' 'Planctomycetes' 'Gemmatimonadetes' 'Candidatus_Saccharibacteria' 'Thaumarchaeota' 'Armatimonadetes' 'Euryarchaeota' 'candidate_division_WPS-1' 'Cyanobacteria/Chloroplast' 'Chlamydiae' 'Nitrospirae' 'Ignavibacteriae' 'Latescibacteria' 'candidate_division_WPS-2' 'Microgenomates' 'Elusimicrobia' 'Spirochaetes' 'Aminicenantes' 'Woesearchaeota'

In [13]:

length(rownames(df))

Out[13]:

25

In [14]:

group = rep(c('A','B'),each = 25*16/2)
length(group)

Out[14]:

400

In [15]:

data$group = group

In [16]:

head(data)

Out[16]:

Abundance sample phylum group

							126573

1 Proteobacteria A
12759 1 Actinobacteria A
18428 1 Bacteroidetes A
16566 1 Acidobacteria A
6665 1 Chloroflexi A
6033 1 Firmicutes A

3. 气泡图绘制

In [16]:

ggplot(data, aes(x = sample, y = phylum, size = Abundance, colour = group)) + geom_point() +
theme_bw() +scale_size(range = c(0,6)) + labs(x = "Sample", y = "")

Out[17]: