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【零基礎(chǔ)學(xué)繪圖】之氣泡圖繪制（六）

發(fā)稿時間：2020-05-29來源：天昊生物

氣泡圖是R語音中的基礎(chǔ)繪圖，可用于展示三個變量之間的關(guān)系的圖表，將一個變量放在x軸，另一個變量放在y軸，而第三個變量則用氣泡的大小來表示。通常用于展示差異基因的表達(dá)情況、轉(zhuǎn)錄因子的分析、物種豐度數(shù)據(jù)的可視化、富集分析展示等。這里我們介紹2種繪制氣泡圖的方法：ggpubr繪制氣泡圖和 ggplot 繪制氣泡圖。

一ggpubr繪制氣泡圖

1. 加載ggpubr包
In [1]:

library(ggpubr)

2. 數(shù)據(jù)讀取由于表頭是數(shù)字，需要添加參數(shù)check.names = FIn [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. 氣泡圖繪制3.1 繪制不帶參數(shù)的氣泡圖In [3]:

ggballoonplot(df)

Out[3]:

3.2 添加和填充顏色In [4]:

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

Out[4]:

3.3 按照值的大小填充顏色，并制定氣泡圖形狀In [5]:

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

Out[5]:

3.4 填充數(shù)值show.label =F 默認(rèn)不填充數(shù)值， show.label =T 填充數(shù)值選擇size參數(shù)固定圖形大小In [6]:

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

Out[6]:

二ggplot2繪制氣泡圖

1. 加載ggplot2包In [7]:

library(ggplot2)

2. 數(shù)據(jù)預(yù)處理stack是堆棧的意思，默認(rèn)按列堆數(shù)據(jù)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

添加分組信息，本次分析將16個樣品分為2組，組名分別未A、BIn [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]:

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]:

In [14]:

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

Out[14]:

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. 氣泡圖繪制

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]: