R中的冲积地块：如何划分地层？

Posted 2023-02-16

【中文标题】R中的冲积地块：如何划分地层？

【英文标题】：Alluvial plot in R: how to space the strata?

【发布时间】：2021-07-10 19:27:17

【问题描述】：

背景

我一直致力于使用ggplot 和ggalluvial package 创建冲积图（一种桑基图），以可视化随时间变化的频率差异及其起源。

例如，我创建了一个包含 100 名假想患者的简单数据集，这些患者接受了 COVID-19 筛查。 在基线时，所有患者的 COVID-19 均为阴性。假设 1 周后，再次对所有患者进行检测：现在，30 名患者为阳性，65 名患者为阴性，5 名结果不确定。又过了一周，30名阳性患者仍为阳性，10名患者由阴性转为阳性，其余均为阴性。

data <- data.frame(analysis = as.factor(rep(c("time0", "time1", "time2"), each = 4)), 
                   freq = rep(c(30, 10, 55, 5), 3), 
                   track = rep(1:4, 3),  
                   response = c("neg","neg","neg","neg", "pos", "neg", "neg", "inconc", "pos", "pos", "neg", "neg"))

#   analysis freq track response
#1     time0   30     1      neg
#2     time0   10     2      neg
#3     time0   55     3      neg
#4     time0    5     4      neg
#5     time1   30     1      pos
#6     time1   10     2      neg
#7     time1   55     3      neg
#8     time1    5     4   inconc
#9     time2   30     1      pos
#10    time2   10     2      pos
#11    time2   55     3      neg
#12    time2    5     4      neg

目标

我们的目标是创建一个冲积图，以可视化这些患者随时间推移的“轨迹”（即冲积层），从而在两周后可视化结果的来源。比如：

尝试

我设法制作了这个数字的主要部分：

library(tidyverse)
library(ggalluvial)

ggplot(data, aes(x = analysis, stratum = response, alluvium = track, y = freq, fill = response), col = "black") +
    geom_flow(stat = "alluvium") +
    geom_stratum(alpha = .5) +
    scale_fill_manual(values = c("grey", "green", "red"))

问题

但是，我无法清楚地区分这些地层。现在，它们都彼此相邻，从而形成一个完全“填充”的矩形。

如何使用R 中的ggalluvial 包在冲积地块中划分地层/冲积层？

【问题讨论】：

检查matthewdharris.com/2017/11/11/…

【参考方案1】：

ggalluvial 包的作者将冲积地块定义为：

Alluvial plots are parallel sets plots in which classes are ordered consistently across dimensions and stacked without gaps at each dimension.

你可能想做一个 sankey plot，一个合理的包是：ggsankey

【参考方案2】：

使用ggalluvial，您可以这样做：

冲积地块的问题是地层上的“脉”之间没有分离。

library(ggplot2)
library(ggalluvial)

data$track <- factor(data$track)


ggplot(data, aes(x = analysis, y = freq, stratum = response, alluvium = track)) +
  geom_flow(aes(fill = track), stat = "alluvium") +
  geom_lode(aes(fill = response))+
  geom_text(stat = "stratum", aes(label = response)) +
  scale_fill_manual("Track",
                    breaks = c("1", "2", "3", "4", "neg", "pos", "inconc" ),
                    labels = c("1", "2", "3", "4", "", "", ""),
                    values = c("grey15", "grey40", "grey65", "grey90", "red", "green", "orange"))+
  guides(fill = guide_legend(override.aes = list(alpha = c(`1` = 1, `2` = 1, `3` = 1, `4` = 1,
                                                          neg = 0, pos = 0, inconc = 0))))+
  theme_minimal()

^{由reprex package (v2.0.0) 于 2021-04-18 创建}