UpSetR error when using queries: replacement has 1 row, data has 0

Question

I have tried to use UpsetR to visualize the input file which can be found here

> library("UpSetR")
> orthogroups_df<- read.table("orthogroups.GeneCount.tsv",  header=T, stringsAsFactors = F)
> #All species
> 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
> orthogroups_df[orthogroups_df > 0] <- 1
> 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)))


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

How is it possible to fix the above error?

Difficult to answer without knowing what `orthogroups_df` looks like. Please [make this question reproducible](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) by including a small representative dataset in a plain text format, or a link to the TSV file. — neilfws, Nov 16 '22 at 04:01
I updated my question but the whole dataset can be found [here](https://cloudstor.aarnet.edu.au/plus/s/OupXC8rF2bDFtRV). — user3523406, Nov 16 '22 at 04:38

score 0 · Accepted Answer · answered Nov 22 '22 at 09:19

We need to set the number of intersects - nintersects - to a higher number so that sets in query params can be shown.

By default nintersects is set to 40, and list("NQLD", "Nlab", "Nsyl") appears after 40 at 90th position, so we need a bigger number, here I tried with 90:

upset(orthogroups_df, 
      nsets = ncol(orthogroups_df), 
      sets = rev(c(selected_species)), 
      nintersects = 90,
      queries = list(
        list(query = intersects,
             params = list("NQLD", "Nlab", "Nsyl"),
             color = "red",
             active = TRUE),
        list(query = intersects, 
             params = list("NQLD", "Nlab"), 
             color = "blue", 
             active = TRUE)))

UpSetR error when using queries: replacement has 1 row, data has 0

1 Answers1