嗨朋友们，我正在使用 Phyloseq 包来分析 16S 宏基因组数据。我想制作一个堆叠的条形图，y 轴有丰富，x 轴有样本。我有 10 个样品，其中 4 个早，6 个晚。我怎样才能在条形图中安排。我的意思是前四个控制条，接下来的六个是肥胖的。我试过重新排序功能。但发现重新排序仅适用于数值而不是非数字的“ealy”和“late”值。这是我的代码：
ggplot(mdata_class, aes(x = Sample, y = Abundance, fill = Class)) +
#facet_grid(time~.) +
geom_bar(stat = "identity") +
scale_fill_manual(values = class_colors) +
scale_x_discrete(
breaks = map$sample,
labels = map$time,
drop = FALSE
) +
# Remove x axis title, and rotate sample labels
theme(axis.title.x = element_blank(),
axis.text.x=element_text(angle=90,hjust=1,vjust=0.5)) +
# additional stuff
guides(fill = guide_legend(reverse = TRUE, keywidth = 1, keyheight = 1)) +
ylab("Relative Abundance (Class > 1%) \n") +
ggtitle("Class Composition of Mothur MiSeq SOP data per individual")
这是我打印时的输出mdata_class
OTU Sample Abundance sample type time bodyweight Kingdom Phylum Class
1 Otu00009 DRR046797 0.10213514 DRR046797 control early 20 k__Bacteria p__Actinobacteria c__Actinobacteria
2 Otu00009 DRR046803 0.08912090 DRR046803 obese late 45 k__Bacteria p__Actinobacteria c__Actinobacteria
3 Otu00009 DRR046798 0.08548668 DRR046798 control early 40 k__Bacteria p__Actinobacteria c__Actinobacteria
4 Otu00009 DRR046801 0.05865369 DRR046801 obese late 45 k__Bacteria p__Actinobacteria c__Actinobacteria
5 Otu00009 DRR046805 0.05629529 DRR046805 obese early 78 k__Bacteria p__Actinobacteria c__Actinobacteria
6 Otu00009 DRR046800 0.05349115 DRR046800 control late 45 k__Bacteria p__Actinobacteria c__Actinobacteria
7 Otu00009 DRR046802 0.02630549 DRR046802 obese late 45 k__Bacteria p__Actinobacteria c__Actinobacteria
8 Otu00020 DRR046804 0.14788058 DRR046804 obese late 45 k__Bacteria p__Firmicutes c__Bacilli
9 Otu00020 DRR046798 0.05880534 DRR046798 control early 40 k__Bacteria p__Firmicutes c__Bacilli
10 Otu00020 DRR046802 0.02007156 DRR046802 obese late 45 k__Bacteria p__Firmicutes c__Bacilli
11 Otu00020 DRR046803 0.01713152 DRR046803 obese late 45 k__Bacteria p__Firmicutes c__Bacilli
12 Otu00020 DRR046797 0.01035021 DRR046797 control early 20 k__Bacteria p__Firmicutes c__Bacilli
13 Otu00002 DRR046799 0.39862975 DRR046799 control late 45 k__Bacteria p__Bacteroidetes c__Bacteroidia
14 Otu00002 DRR046797 0.36894936 DRR046797 control early 20 k__Bacteria p__Bacteroidetes c__Bacteroidia
15 Otu00002 DRR046800 0.35967465 DRR046800 control late 45 k__Bacteria p__Bacteroidetes c__Bacteroidia
16 Otu00002 DRR046804 0.34913663 DRR046804 obese late 45 k__Bacteria p__Bacteroidetes c__Bacteroidia
17 Otu00002 DRR046805 0.33464421 DRR046805 obese early 78 k__Bacteria p__Bacteroidetes c__Bacteroidia
18 Otu00002 DRR046798 0.33061613 DRR046798 control early 40 k__Bacteria p__Bacteroidetes c__Bacteroidia
19 Otu00002 DRR046803 0.26273936 DRR046803 obese late 45 k__Bacteria p__Bacteroidetes c__Bacteroidia
20 Otu00002 DRR046801 0.26121922 DRR046801 obese late 45 k__Bacteria p__Bacteroidetes c__Bacteroidia
21 Otu00002 DRR046806 0.18225234 DRR046806 obese early 32 k__Bacteria p__Bacteroidetes c__Bacteroidia
22 Otu00002 DRR046802 0.17431231 DRR046802 obese late 45 k__Bacteria p__Bacteroidetes c__Bacteroidia
23 Otu00035 DRR046798 0.01992751 DRR046798 control early 40 k__Bacteria p__Proteobacteria c__Betaproteobacteria
24 Otu00035 DRR046799 0.01478939 DRR046799 control late 45 k__Bacteria p__Proteobacteria c__Betaproteobacteria
25 Otu00035 DRR046803 0.01371867 DRR046803 obese late 45 k__Bacteria p__Proteobacteria c__Betaproteobacteria
26 Otu00035 DRR046804 0.01245559 DRR046804 obese late 45 k__Bacteria p__Proteobacteria c__Betaproteobacteria
27 Otu00035 DRR046801 0.01083689 DRR046801 obese late 45 k__Bacteria p__Proteobacteria c__Betaproteobacteria
28 Otu00001 DRR046806 0.66847252 DRR046806 obese early 32 k__Bacteria p__Firmicutes c__Clostridia
29 Otu00001 DRR046802 0.66746338 DRR046802 obese late 45 k__Bacteria p__Firmicutes c__Clostridia
30 Otu00001 DRR046801 0.63904709 DRR046801 obese late 45 k__Bacteria p__Firmicutes c__Clostridia
31 Otu00001 DRR046803 0.57818463 DRR046803 obese late 45 k__Bacteria p__Firmicutes c__Clostridia
32 Otu00001 DRR046800 0.56657288 DRR046800 control late 45 k__Bacteria p__Firmicutes c__Clostridia
33 Otu00001 DRR046799 0.56348693 DRR046799 control late 45 k__Bacteria p__Firmicutes c__Clostridia
34 Otu00001 DRR046805 0.54092091 DRR046805 obese early 78 k__Bacteria p__Firmicutes c__Clostridia
35 Otu00001 DRR046797 0.47789350 DRR046797 control early 20 k__Bacteria p__Firmicutes c__Clostridia
36 Otu00001 DRR046798 0.47385673 DRR046798 control early 40 k__Bacteria p__Firmicutes c__Clostridia
37 Otu00001 DRR046804 0.44762754 DRR046804 obese late 45 k__Bacteria p__Firmicutes c__Clostridia
38 Otu00014 DRR046802 0.06449178 DRR046802 obese late 45 k__Bacteria p__Actinobacteria c__Coriobacteriia
39 Otu00014 DRR046805 0.03359757 DRR046805 obese early 78 k__Bacteria p__Actinobacteria c__Coriobacteriia
40 Otu00014 DRR046797 0.03141518 DRR046797 control early 20 k__Bacteria p__Actinobacteria c__Coriobacteriia
41 Otu00014 DRR046803 0.03140499 DRR046803 obese late 45 k__Bacteria p__Actinobacteria c__Coriobacteriia
42 Otu00014 DRR046804 0.01792293 DRR046804 obese late 45 k__Bacteria p__Actinobacteria c__Coriobacteriia
43 Otu00014 DRR046806 0.01570523 DRR046806 obese early 32 k__Bacteria p__Actinobacteria c__Coriobacteriia
44 Otu00014 DRR046801 0.01404050 DRR046801 obese late 45 k__Bacteria p__Actinobacteria c__Coriobacteriia
45 Otu00058 DRR046802 0.03083417 DRR046802 obese late 45 k__Bacteria p__Firmicutes c__Erysipelotrichi
46 Otu00058 DRR046805 0.01128693 DRR046805 obese early 78 k__Bacteria p__Firmicutes c__Erysipelotrichi
47 Otu00031 DRR046806 0.09179629 DRR046806 obese early 32 k__Bacteria p__Fusobacteria c__Fusobacteriia
48 Otu00066 DRR046798 0.02033571 DRR046798 control early 40 k__Bacteria p__Proteobacteria c__Gammaproteobacteria
这是我打印的时候map
Sample Data: [10 samples by 4 sample variables]:
sample type time bodyweight
DRR046797 DRR046797 control early 20
DRR046798 DRR046798 control early 40
DRR046799 DRR046799 control late 45
DRR046800 DRR046800 control late 45
DRR046801 DRR046801 obese late 45
DRR046802 DRR046802 obese late 45
DRR046803 DRR046803 obese late 45
DRR046804 DRR046804 obese late 45
DRR046805 DRR046805 obese early 78
DRR046806 DRR046806 obese early 32
谢谢和问候， DC7