ggalluvial|TCGA临床数据绘制桑基图（Sankey）
桑基图（Sankey diagram），是一种特定类型的流程图，图中延伸的分支的宽度对应数据流量的大小，通常应用于能源、材料成分、金融等数据的可视化分析。
因1898年Matthew Henry Phineas Riall Sankey绘制的“蒸汽机的能源效率图”而闻名，此后便以其名字命名为“桑基图”。
一 载入R包，数据
本文使用TCGA数据集中的LIHC的临床数据进行展示，大家可以根据数据格式处理自己的临床数据。也可后台回复“R-桑基图”获得示例数据以及R代码。
#install.packages("ggalluvial")
library(ggalluvial)
library(ggplot2)
library(dplyr)
#读入LIHC临床数据
LIHC <- read.csv("TCGA_lihc.csv",header=TRUE)
#展示数据情况
head(LIHC)
PATIENT_ID AGE SEX AJCC_PATHOLOGIC_TUMOR_STAGE OS_STATUS
1 TCGA-XR-A8TE less50 Male STAGE III LIVING
2 TCGA-5R-AA1D less50 Female STAGE III LIVING
3 TCGA-DD-A1EC less50 Female STAGE I LIVING
4 TCGA-ED-A7PY less50 Female STAGE II LIVING
5 TCGA-RC-A6M5 less50 Female STAGE IV LIVING
6 TCGA-DD-A1EH less50 Male STAGE III LIVING
summary(LIHC)
桑基图的数据结构需要节点，权重等信息，ggalluvial 的输入数据可以是长数据亦可以是宽数据。
二 绘制桑基图
1 宽数据示例
对临床数据进行简单的处理，得到后四个变量的频数，整理成宽数据：以下处理过程可参考链接
#分组计算频数
LIHCData <- group_by(data,AGE,SEX,AJCC_PATHOLOGIC_TUMOR_STAGE,OS_STATUS) %>% summarise(., count = n())
#查看宽数据格式
head(LIHCData)
AGE SEX AJCC_PATHOLOGIC_TUMOR_STAGE OS_STATUS count
<fct> <fct> <fct> <fct> <int>
1 50to70 Female STAGE I DECEASED 11
2 50to70 Female STAGE I LIVING 16
3 50to70 Female STAGE II DECEASED 3
4 50to70 Female STAGE II LIVING 11
5 50to70 Female STAGE III DECEASED 8
6 50to70 Female STAGE III LIVING 9
绘制桑基图
ggplot(as.data.frame(LIHCData),
aes(axis1 = AJCC_PATHOLOGIC_TUMOR_STAGE, axis2 = SEX, axis3 = AGE,
y= count)) +
scale_x_discrete(limits = c("AJCC_STAGE", "SEX", "AGE"), expand = c(.1, .05)) +
geom_alluvium(aes(fill = OS_STATUS)) +
geom_stratum() + geom_text(stat = "stratum", label.strata = TRUE) +
theme_minimal() +
ggtitle("Patients in the TCGA-LIHC cohort",
"stratified by demographics and survival")
-
axis参数设置待展示的节点信息（柱子）；
-
geom_alluvium参数设置组间面积连接，此处按生存状态分组；
2 长数据示例
ggplot2通常处理的都是长表格模式，使用to_lodes_form函数即可转换
#to_lodes_form会生成alluvium和stratum列。主分组位于命名的key列中
LIHC_long <- to_lodes_form(data.frame(LIHCData),
key = "Demographic",
axes = 1:3)
head(LIHC_long)
OS_STATUS count alluvium Demographic stratum
1 DECEASED 11 1 AGE 50to70
2 LIVING 16 2 AGE 50to70
3 DECEASED 3 3 AGE 50to70
4 LIVING 11 4 AGE 50to70
5 DECEASED 8 5 AGE 50to70
6 LIVING 9 6 AGE 50to70
# 绘制桑基图
ggplot(data = LIHC_long,
aes(x = Demographic, stratum = stratum, alluvium = alluvium,
y = count, label = stratum)) +
geom_alluvium(aes(fill = OS_STATUS)) +
geom_stratum() + geom_text(stat = "stratum") +
theme_minimal() +
ggtitle("Patients in the TCGA-LIHC cohort",
"stratified by demographics and survival")
3 状态变化的趋势
vaccinations为R包内置数据集，可展示同一subject在不同survey状态下的response情况。
data(vaccinations)
levels(vaccinations$response) <- rev(levels(vaccinations$response))
ggplot(vaccinations,
aes(x = survey, stratum = response, alluvium = subject,
y = freq,
fill = response, label = response)) +
scale_x_discrete(expand = c(.1, .1)) +
geom_flow() +
geom_stratum(alpha = .5) +
geom_text(stat = "stratum", size = 3) +
theme(legend.position = "none") +
ggtitle("vaccination survey responses at three points in time")
4 更多细节
vignette(topic = "ggalluvial", package = "ggalluvial")
以上就是如何使用R-ggalluvial包绘制桑基图的简单介绍，可以自己动手展示了 🤭。
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