使用UpSetR绘图时出现start_col:end_col参数长度为0错误的解决咨询

问题场景 #

使用如下数据集：

df <- structure(list(id = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 
13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 
29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40), a = c(0, 0, 
0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 
1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0), b = c(1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1), c = c(0, 
0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 
1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0), d = c(1, 
1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 
0, 0, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0), e = c(0, 
0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), class = c("tbl_df", 
"tbl", "data.frame"), row.names = c(NA, -40L))

执行以下UpSetR绘图代码时触发报错：

library(UpSetR)
graph <- upset(df,
               sets = c("a", "b", "c", "d", "e"),
               order.by = "freq",
               empty.intersections = "on")

报错及警告信息：

Error in start_col:end_col : argument of length 0
In addition: There were 12 warnings (use warnings() to see them)
Warning messages:
1: In xtfrm.data.frame(x) : cannot xtfrm data frames
2: In xtfrm.data.frame(x) : cannot xtfrm data frames
3: In xtfrm.data.frame(x) : cannot xtfrm data frames
4: In xtfrm.data.frame(x) : cannot xtfrm data frames
5: In xtfrm.data.frame(x) : cannot xtfrm data frames
6: In xtfrm.data.frame(x) : cannot xtfrm data frames
7: In xtfrm.data.frame(x) : cannot xtfrm data frames
8: In xtfrm.data.frame(x) : cannot xtfrm data frames
9: In xtfrm.data.frame(x) : cannot xtfrm data frames
10: In xtfrm.data.frame(x) : cannot xtfrm data frames
11: In xtfrm.data.frame(x) : cannot xtfrm data frames
12: In xtfrm.data.frame(x) : cannot xtfrm data frames

问题根源 #

你的数据集是tibble（tbl_df类型），UpSetR包对tibble的兼容性较差，而官方示例使用的是普通data.frame，这是触发报错的核心原因。

解决方法 #

将tibble转换为普通data.frame后再调用upset()函数，修改后的代码如下：

library(UpSetR)
# 转换为普通data.frame
df <- as.data.frame(df)
# 重新绘制UpSet交集图
graph <- upset(df,
               sets = c("a", "b", "c", "d", "e"),
               order.by = "freq",
               empty.intersections = "on")

执行上述代码后即可正常生成交集可视化图，不会再触发原报错和警告。

内容的提问来源于stack exchange，提问作者user19745561