以箱图和散点图为例，给ggplot散点添加配对连线。方法使用简单，就是geom_line(aes(group = pair))即可。给geom_point添加配对连线时需要使用position_dodge函数配置线端点位置与点一致。

一、箱图：添加散点，连线

1 输入格式

id  group   Completeness
AF04-12 BGISEQ  99.25
AF04-12 Illumina    98.76
AF04-17 BGISEQ  99.46
AF04-17 Illumina    98.9
AF04-28 BGISEQ  93.55
AF04-28 Illumina    93.55
AF11-25B    BGISEQ  99.54
AF11-25B    Illumina    99.08

2 wilcox分析和绘图代码

##  complete
library("ggplot2")
data = read.table("data.txt", header=T, sep="\t")
## wilcox
bgi = data[data$group=="BGISEQ",]$Completeness
illu = data[data$group=="Illumina",]$Completeness
mean(bgi)
mean(illu)
wilcox.test(bgi, illu, paired = TRUE)

##
Title = "Wilcoxon p value < 2.5e-13"
p = ggplot(data, aes(x = group, y = Completeness, color=group)) + 
  labs(x="", y="Completeness (%)", title=Title) +
  theme_classic() +
  geom_boxplot(width=0.5, outlier.colour = NA, lwd = 1) +
  geom_line(aes(group=id), color="gray" ,position = position_dodge(0.2)) +
  geom_point(aes(fill=group, group=id), 
             size = 2, 
             position = position_dodge(0.2)) +
  scale_fill_manual(values = c('orangered3','deepskyblue3')) +
  theme(panel.grid = element_line(colour = 'white')) +
  theme(legend.position="none") +
  theme(axis.title = element_text(size = 30),
        axis.text = element_text(size = 28),
        axis.line = element_line(size = 1),
        axis.ticks = element_line(size = 1),
        title = element_text(size = 20))

ggsave(p, filename="complete.png")

二、PCOA散点图：添加散点，连线

1 输入数据格式

  id    group Completeness Contamination    gc contigs largest  length
1 AF04_12   BGISEQ        99.25          0.13 42.03     143  332931 5076534
2 AF04_12 Illumina        98.76          0.13 42.00     136  365905 5105661
3 AF04_17   BGISEQ        99.46          0.08 41.99     106  412791 6672015
4 AF04_17 Illumina        98.90          0.08 41.98     104  386819 6663758
5 AF04_28   BGISEQ        93.55          0.61 42.57      36  744099 4803502
6 AF04_28 Illumina        93.55          1.99 42.54      36  616477 4874474
     N50 N_per_100_kbp Genome_fraction
1  80303          4.14          99.061
2  83739          9.01          99.634
3 140135          1.05          99.899
4 137940          4.53          99.763
5 363431        696.22          97.450
6 363455         13.13          99.569

2 绘图数据格式

> head(pcoa_point)
      Axis.1      Axis.2 Platform    pair
1 -0.1485042  0.08032245   BGISEQ AF04_12
2 -0.1490304  0.07219616 Illumina AF04_12
3 -0.2436660  0.02873192   BGISEQ AF04_17
4 -0.2445737  0.03555739 Illumina AF04_17
5 -0.1109480 -0.05709881   BGISEQ AF04_28
6 -0.1157950 -0.03534015 Illumina AF04_28

3 PCOA分析，画图代码

library(vegan)
library(ape)
setwd("../pcoa/")

data = read.table("data.txt", sep="\t", header=T)
input = data[, c(-1, -2)]

veg = vegdist(input, method = "bray")
pcoa = pcoa(veg)

pcoa_point = data.frame(pcoa$vectors[, c(1, 2)], Platform = data$group, pair = data$id)
#write.csv(pcoa_point, file="pcoa_bc.csv")
    
xylab = paste(c("PCoA1: ", "PCoA2: "), round(pcoa$values$Relative_eig[1:2]*100, 2), "%", sep = "")

# https://datavizpyr.com/connect-paired-points-with-lines-in-scatterplot-in-ggplot2/
result = 
ggplot(pcoa_point, aes(x=Axis.1, y=Axis.2, color=Platform)) +
  geom_point(pch=19, size=4) + 
  stat_ellipse(level = 0.95, show.legend = F, aes(color=Platform)) +
  geom_line(aes(group = pair), color = "grey") +
  theme_classic() +
  labs(x=xylab[1], y=xylab[2], title = paste('Bray-Curtis PCoA')) +
  theme(legend.background = element_rect(color = "black", linetype = "solid", size = 1)) +
  theme(legend.text=element_text(size=15)) +
  theme(legend.title=element_text(face='bold', size=20)) +
  #theme(text=element_text(family="serif")) +
  theme(axis.title = element_text(size = 20)) +
  theme(axis.text = element_text(size = 15),
        axis.line = element_line(size = 1),
        axis.ticks = element_line(size = 1)) +
  theme(plot.title = element_text(face="bold", size=16)) +
  scale_fill_manual(
    values = c("BGISEQ" = "orangered3",
    "Illumina" = "deepskyblue3")) +
  scale_color_manual(
    values = c("BGISEQ" = "orangered3",
    "Illumina" = "deepskyblue3"))

ggsave(result, filename="pcoa_bc.png", width = 8)

三、棒棒糖图

1 输入数据格式

        id length_bgi length_illumina illumina_minus_bgi           Genus
1  AF04-12       1524            1524                  0     Bacteroides
2  AF04-17       1525            1525                  0     Bacteroides
3  AF04-28        992            1525                533     Bacteroides
4 AF11-25B       1434            1526                 92 Bifidobacterium
5  AF13-35       1545            1545                  0   Streptococcus
6  AF14-49       1522             984               -538   Butyricimonas

2 数据处理及绘图代码

library(ggplot2)
df = read.table("data.txt", header=T, sep="\t")

data = df[order(df$length_bgi, decreasing=T), c(1,2,3)]
input = melt(data, id='id')
input$id = factor(input$id, levels = c(unique(input$id)))

result = 
ggplot(input, aes(x=value, y=id)) +
geom_line(aes(group = id)) +
geom_point(aes(color = variable), size=4) +
theme(legend.position="top")

ggsave(result, file="test.pdf", height = 14)

参考更多：
How To Connect Paired Points with Lines in Scatterplot in ggplot2?
https://datavizpyr.com/dumbbell-plot-in-r-with-ggplot2/