UpSetR plot of Orthofinder results failed
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Entering edit mode
8 days ago
Ric ▴ 420

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?

upsetR r orthofinder plot • 159 views
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Entering edit mode

Crossposted at Stackoverflow, see my answer there, we need to set nintersects to a higher number to include our query params columns.

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0
Entering edit mode

There is no single intersection unique to "NQLD" and "Nlab" and "Nsyl" exclusively

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That's what I thought as well, but there are plenty of intersection on those 3 columns. The issue the nintersects which is set to 40 by default, and query intersect appears at 90th position.

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