如何在R中创建一个sankey图，显示同一节点随时间的变化？

Question

我正在尝试创建我的数据的Sankey图 - 我的数据的输入在下面提供。

dput(df_new)
structure(list(Hospital = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 
2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 
5, 5, 5, 5), Patient = c(21, 21, 21, 21, 21, 21, 21, 21, 21, 
21, 21, 21, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 24, 
24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 
25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 
26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 
27, 27, 27, 27, 27), Therapy = c("Etanercept", "Etanercept", 
"Etanercept", "Etanercept", "Etanercept", "Etanercept", "Infliximab", 
"Infliximab", "Infliximab", "Infliximab", "Infliximab", "Infliximab", 
"Etanercept", "Etanercept", "Etanercept", "Etanercept", "Etanercept", 
"Etanercept", "Rituximab", "Rituximab", "Rituximab", "Rituximab", 
"Rituximab", "Rituximab", "Adalimumab", "Adalimumab", "Adalimumab", 
"Adalimumab", "Adalimumab", "Adalimumab", "Infliximab", "Infliximab", 
"Infliximab", "Infliximab", "Infliximab", "Infliximab", "Etanercept", 
"Etanercept", "Etanercept", "Etanercept", "Etanercept", "Etanercept", 
"Infliximab", "Infliximab", "Infliximab", "Infliximab", "Infliximab", 
"Infliximab", "Etanercept", "Etanercept", "Etanercept", "Etanercept", 
"Etanercept", "Etanercept", "Rituximab", "Rituximab", "Rituximab", 
"Rituximab", "Rituximab", "Rituximab", "Adalimumab", "Adalimumab", 
"Adalimumab", "Adalimumab", "Adalimumab", "Adalimumab", "Etanercept", 
"Etanercept", "Etanercept", "Etanercept", "Etanercept", "Etanercept", 
"Infliximab", "Infliximab", "Infliximab", "Infliximab", "Infliximab", 
"Infliximab"), `First,Second,Third,Fourth,etc` = c(1, 1, 1, 1, 
1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 1, 
1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4), QualityLife = c(3, 4, 4, 4, 
2, 2, 2, 5, 6, 6, 6, 8, 1, 3, 3, 4, 4, 5, 3, 5, 6, 6, 7, 7, 2, 
3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 2, 3, 3, 3, 4, 4, 1, 3, 3, 3, 
1, 2, 2, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 3, 3, 3, 4, 4, 2, 
3, 3, 3, 4, 4, 3, 3, 3, 4, 4, 5), FollowUp_time = c(0, 1, 3, 
6, 12, 18, 0, 1, 3, 6, 12, 18, 0, 1, 3, 6, 12, 18, 0, 1, 3, 6, 
12, 18, 0, 1, 3, 6, 12, 18, 0, 1, 3, 6, 12, 18, 0, 1, 3, 6, 12, 
18, 0, 1, 3, 6, 12, 18, 0, 1, 3, 6, 12, 18, 0, 1, 3, 6, 12, 18, 
0, 1, 3, 6, 12, 18, 0, 1, 3, 6, 12, 18, 0, 1, 3, 6, 12, 18), 
    Continuous_time = c(0, 1, 3, 6, 12, 18, 18, 19, 21, 24, 30, 
    36, 0, 1, 3, 6, 12, 18, 0, 1, 3, 6, 12, 18, 0, 1, 3, 6, 12, 
    18, 36, 37, 39, 42, 48, 54, 0, 1, 3, 6, 12, 18, 0, 1, 3, 
    6, 12, 18, 54, 55, 57, 60, 66, 72, 90, 91, 93, 96, 102, 108, 
    126, 127, 129, 132, 138, 144, 0, 1, 3, 6, 12, 18, 72, 73, 
    75, 78, 84, 90)), row.names = c(NA, -78L), class = "data.frame")

这是一项保健活动。对于每种治疗患者，在0,1,3,6,12,18个月被问及他们的生活质量如何。如果在特定的随访时间，生活质量<特定参数，医生改变患者的治疗，我想在Sankey图中显示。我希望有一个节点“治疗”（具有不同治疗名称的分类变量）随时间重复，x轴考虑时间。谁能帮我这个？我非常感谢任何帮助。

这是我到目前为止所尝试的：

### install and load packages
install.packages("ggplot2")
install.packages("readxl")
install.packages("ggforce")

# load packages
library(ggplot2)
library(readxl)
library(ggforce)

### read dataset
dataset_new <- read_excel("Made_up_dataset_new.xlsx")
df_new <- as.data.frame(dataset_new)

df_new$Unit <- 1

df_sankey <- df_new[c("Therapy", "First,Second,Third,Fourth,etc", "Continuous_time","Unit")]

# transform dataframe into appropriate format
df_sankey <- gather_set_data(df_sankey, 1:3)

# define axis-width / sep parameters once here, to be used by each geom layer in the plot
aw <- 0.1
sp <- 0.1

ggplot(df_sankey, 
       aes(x = x, id = id, split = y, value = Unit)) +
  geom_parallel_sets(aes(fill = Therapy), alpha = 0.3, 
                     axis.width = aw, sep = sp) +
  geom_parallel_sets_axes(axis.width = aw, sep = sp) +
  geom_parallel_sets_labels(colour = "white", 
                            angle = 0, size = 3,
                            axis.width = aw, sep = sp) +
  theme_minimal()

但结果不是我想要的，因为时间在y轴上压缩，而不是在x轴上，如果这有意义的话？请在下面找到我认为的草稿：

我感谢任何帮助！

---

根据下面的答案，我试图使代码适应我的数据集，我运行：

df_sankey <- df_new[c("Patient","FirstSecondThird","Therapy")]
head(df_sankey)

df_new$FirstSecondThird <- factor(df_new$FirstSecondThird)

# Plotting it
ggplot(df_sankey, aes(x = FirstSecondThird, stratum = Therapy, alluvium = Patient, fill = Therapy, label = Therapy)) +
  scale_fill_brewer(type = "qual", palette = "Set2") +
  geom_flow(stat = "alluvium", lode.guidance = "rightleft", color = "darkgray") +
  geom_stratum() +
  theme(legend.position = "bottom") +
  ggtitle("Treatment across observation period")

结果显示在下面，但这并不是我想要的（因为我试图在附加的草案中解释，我知道这是非常基本的）：

Answer 1

嗯，你有几种选择。对我有用的第一个解决方案是ggplot / geom_flow：

# requires(ggplot2)
# requires(ggalluvial)

# faking the data for 20 patients
set.seed(42)
individual <- as.character(rep(1:20,each=5))
timeperiod <- paste0(rep(c(0, 18,36,54,72),20),"_week")
therapy <- factor(sample(c("Etanercept", "Infliximab", "Rituximab",  "Adalimumab","Missing"), 100, replace=T))
d <- data.frame(individual, timeperiod, therapy)
head(d)

# Plotting it
ggplot(d, aes(x = timeperiod, stratum = therapy, alluvium = individual, fill = therapy, label = therapy)) +
  scale_fill_brewer(type = "qual", palette = "Set2") +
  geom_flow(stat = "alluvium", lode.guidance = "rightleft", color = "darkgray") +
  geom_stratum() +
  theme(legend.position = "bottom") +
  ggtitle("Treatment across observation period")

stat = "alluvium"中的geom_flow论证应该允许跟踪个别患者，但如果你愿意，你也可以合并流量：

ggplot(d, aes(x = timeperiod, stratum = therapy, alluvium = individual, fill = therapy, label = therapy)) +
  scale_fill_brewer(type = "qual", palette = "Set2") +
  geom_flow(color = "darkgray") +
  geom_stratum() +
  theme(legend.position = "bottom") +
  ggtitle("Treatment across observation period")

编辑1：如果您希望某些患者停止流程（例如治疗已经完成），您可以通过将这些患者设置为NA来轻松实现：

# setting 3 pantients as NA for the last timepoint
d[which(d$individual==3 & d$timeperiod=="72_week"), ]["therapy"] <- NA 
d[which(d$individual==6 & d$timeperiod=="72_week"), ]["therapy"] <- NA 
d[which(d$individual==9 & d$timeperiod=="72_week"), ]["therapy"] <- NA 

# making the plot:
ggplot(d, aes(x = timeperiod, stratum = therapy, alluvium = individual, fill = therapy, label = therapy)) +
scale_fill_brewer(type = "qual", palette = "Set2") +
geom_flow(stat = "alluvium", lode.guidance = "rightleft", color = "darkgray") + 
geom_stratum(alpha=0.75) +
theme(legend.position = "bottom") +
ggtitle("Treatment across observation period")

现在，说实话，networkD3工作，但我只是没有设法让它看起来很好。

编辑2：

• 您也可以使用geom_alluvium而不是geom_flow。它们之间的主要（视觉）差异在于，在geom_flow中，流的颜色是从相邻节点（源或目标）继承的。在geom_alluvium中，它继承自第一个节点 - 例如当通过节点时，流不会改变颜色。
• 如果你想将图表与另一个图组合，最简单的方法似乎是使用par(mfrow=c(1,2))。