UpSetR调用queries时出现'replacement has 1 row, data has 0'错误的解决方法

问题背景 #

使用UpSetR分析正交组基因计数数据时，执行可视化代码后触发维度不匹配错误。

执行代码及数据预览 #

library("UpSetR")
orthogroups_df<- read.table("orthogroups.GeneCount.tsv",  header=T, stringsAsFactors = F)
# 提取所有物种列
selected_species <- colnames(orthogroups_df)[2:(ncol(orthogroups_df) -1)] 
selected_species
 [1] "Atha" "Cann" "NQLD" "Natt" "Ngla" "Nlab" "Nsyl" "Ntab" "Ntom" "Slyc" "Stub" "Vvin"
head(orthogroups_df)
  Orthogroup Atha Cann NQLD Natt Ngla Nlab Nsyl Ntab Ntom Slyc Stub Vvin Total
1  OG0000000    0    0  965    0    0    3    0    0    0    0    0    0   968
2  OG0000001    0    1    3    0    0  448    0    0    0    0    0    0   452
3  OG0000002    0    1  313    0    0  120    1    0    1    0    0    0   436
4  OG0000003    0   93   15   21   46   16   33   63   36   25   39   26   413
5  OG0000004    1   42    2   34  109    6    8  154   11    9    4    0   380
6  OG0000005    0    2   61    1   34   44   91   70   43   20    1    0   367
ncol(orthogroups_df)
[1] 14
# 转换为二元矩阵
orthogroups_df[orthogroups_df > 0] <- 1
# 执行可视化
upset(orthogroups_df, 
      nsets = ncol(orthogroups_df), 
      sets = rev(c(selected_species)), 
      queries = list(list(query = intersects, params = list("NQLD", "Nlab", "Nsyl"), color = "#238c45", active = T),
                list(query = intersects, params = list("NQLD", "Nlab"), color = "#ffd977", active = T)))

报错信息 #

Error in `$<-.data.frame`(`*tmp*`, "freq", value = 45L) : 
  replacement has 1 row, data has 0

问题原因及修复方案 #

1. 错误根源 #

nsets参数设置错误：数据框共14列，但其中Orthogroup（分组ID）和Total（计数总和）并非物种集合列，实际参与可视化的物种列只有12个。nsets必须与sets指定的列数一致，否则会导致内部数据处理时维度不匹配，触发报错。

2. 修复后的代码 #

library("UpSetR")
orthogroups_df<- read.table("orthogroups.GeneCount.tsv",  header=T, stringsAsFactors = F)
# 提取所有物种列
selected_species <- colnames(orthogroups_df)[2:(ncol(orthogroups_df) -1)] 
# 单独构建仅包含物种列的二元矩阵，避免无关列干扰
orthogroups_binary <- orthogroups_df[, selected_species]
orthogroups_binary[orthogroups_binary > 0] <- 1

# 执行可视化，nsets设置为物种列的数量
upset(orthogroups_binary, 
      nsets = length(selected_species), 
      sets = rev(selected_species), 
      queries = list(list(query = intersects, params = list("NQLD", "Nlab", "Nsyl"), color = "#238c45", active = TRUE),
                list(query = intersects, params = list("NQLD", "Nlab"), color = "#ffd977", active = TRUE)))

额外说明 #

• 优先提取物种列构建独立的二元矩阵，可避免Orthogroup和Total列干扰UpSetR的数据解析逻辑。
• 如果需要保留Orthogroup列用于后续标识，可将其添加到二元矩阵中（不影响可视化效果）。

内容的提问来源于stack exchange，提问作者user3523406