最近有朋友問R中繪制沖積圖的代碼，其本質仍然是條形圖只是添加了樣本間的連線；案例要求按列計算每個樣本的相對豐度跟往常有所不同。下面小編就來簡單介紹一下代碼
加載R包
library(tidyverse)
library(ggsci)
library(magrittr)
library(reshape)
library(RColorBrewer)
library(ggalluvial)
導入數據
df <- read_tsv("genus.xls") %>% column_to_rownames(var="ID")
數據清洗
# 按列求和單獨計算每列的相對豐度
df_new <- df %>% mutate_all(~ . / sum(.)) %>%
rownames_to_column(var="Genus")
整合數據
# 將分組文件與豐度表進行整合
plot <- df_new %>% pivot_longer(-Genus) %>%
left_join(.,read_tsv("group.xls"),by=c("name"="sample"))
繪制沖積圖
ggplot(plot, aes(name, value, alluvium = Genus, stratum = Genus)) + # 創建繪圖對象，設置x軸、y軸、alluvium和stratum變量為name、value、Genus
geom_alluvium(aes(fill = Genus), alpha = .5, width = 0.6) + # 添加alluvium圖層，設置填充顏色為Genus，透明度為0.5，寬度為0.6
geom_stratum(aes(fill = Genus), width = 0.6) + # 添加stratum圖層，設置填充顏色為Genus，寬度為0.6
facet_grid(. ~ group, scales = "free", space = "free_x") + # 根據group變量進行網格分面，設置自由的x軸和y軸刻度，自由的x軸間距
labs(x = NULL, y = NULL) + # 設置x軸標簽和y軸標簽為空
scale_fill_simpsons() + # 設置填充顏色的比例尺為Simpsons風格
scale_y_continuous(expand = c(0, 0)) + # 設置y軸刻度范圍的擴展為0
scale_x_discrete(expand = c(0, 0)) + # 設置x軸刻度范圍的擴展為0
theme(
axis.line.x = element_line(color = "black"), # 設置x軸線的顏色為黑色
axis.line.y = element_line(color = "black"), # 設置y軸線的顏色為黑色
axis.text.x = element_text(size = 8,face = "plain",angle = 0,
vjust = 0.5,hjust = 0.5,color = "black"), # 設置x軸文本的大小、樣式、角度、垂直和水平對齊方式，顏色為黑色
axis.text.y = element_text(size = 8, face = "plain", color = "black"), # 設置y軸文本的大小、樣式，顏色為黑色
panel.border = element_blank(), # 設置面板邊框為空白
plot.background = element_blank(), # 設置繪圖區背景為空白
axis.title.x = element_text(margin = margin(t = 10), size = 11, color = "black"), # 設置x軸標題的邊距、大小，顏色為黑色
axis.title.y = element_text(margin = margin(r = 10), size = 11, color = "black"), # 設置y軸標題的邊距、大小，顏色為黑色
panel.grid.major.x = element_blank(), # 設置x軸主要網格線為空白
panel.grid.minor.x = element_blank(), # 設置x軸次要網格線為空白
panel.grid.minor.y = element_blank(), # 設置y軸次要網格線為空白
panel.grid.major.y = element_blank(), # 設置y軸主要網格線為空白
plot.margin = unit(c(0.5, 0.5, 0.5, 0.5), units = "cm"), # 設置繪圖區邊距為0.5厘米
legend.text = element_text(size = 8, color = "black"), # 設置圖例文本的大小和顏色
legend.key = element_blank(), # 設置圖例鍵為空白
legend.title = element_blank(), # 設置圖例標題為空白
panel.background = element_rect(fill = "white"), # 設置面板背景為白色
legend.background = element_rect(color = "black",fill = "transparent",
size = 2,linetype = "blank"), # 設置圖例背景的邊框顏色為黑色，填充為透明，邊框大小為2，線型為空白
panel.spacing.x = unit(0.1, "cm"), # 設置面板x軸間距為0.1厘米
strip.background = element_blank(), # 設置分面標簽背景為空白
strip.text = element_text(color = "black", face = "bold"), # 設置分面標簽文本的顏色為黑色，樣式為粗體
legend.key.height = unit(0.5, "cm"), # 設置圖例鍵的高度為0.5厘米
legend.key.width = unit(0.5, "cm"), # 設置圖例鍵的寬度為0.5厘米
legend.spacing.x = unit(0.1, "cm"), # 設置圖例水平間距為0.1厘米
legend.box.background = element_blank() # 設置圖例框背景為空白
)
