Manually order the set fails in UpsetR
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7 weeks ago
Ric ▴ 430

I have tried to use UpsetR to visualise the input file, which can be found here. How is it possible to make UpsetR accept an order defined in sets=c("Nlab", "NQLD", "Ngla", "Nsyl", "Ntom", "Ntab", "Natt", "Cann", "Stub", "Slyc", "Vvin", "Atha")?

with keep.order = T with keep.order = T

with keep.order = F with keep.order = F

> 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
> # we only show intersections of interest ,  
> intersections=list(list(selected_species),
+                    list("NQLD", "Ngla", "Natt", "Nlab", "Nsyl", "Ntab", "Ntom"),
+                    list("Stub", "Slyc"),
+                    list("Atha", "Vvin"),
+                    list("Ntab", "Nsyl", "Ntom"),
+                    list("Nlab", "NQLD", "Ngla"), 
+                    list("Nlab", "NQLD", "Nsyl"), 
+                    list("Nlab", "Ngla", "Nsyl"), 
+                    list("NQLD", "Nsyl", "Ngla"))
> upset(orthogroups_df, 
+       text.scale = c(1.4),
+       sets=c("Nlab", "NQLD", "Ngla", "Nsyl", "Ntom", "Ntab", "Natt", "Cann", "Stub", "Slyc", "Vvin", "Atha"), 
+       order.by = "freq",
+       keep.order=T, 
+       intersections = intersections, 
+       sets.x.label="Total number of orthogroups", 
+       mainbar.y.label = "Number of orthogroups") 
r ggplot2 upsetr • 412 views
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That top one has your sets in the reverse of the order of your list. It worked.

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It only partly has the reverse order compared to "Nlab", "NQLD", "Ngla", "Nsyl", "Ntom", "Ntab", "Natt", "Cann", "Stub", "Slyc", "Vvin", "Atha". Unfortunately, I can't figure out what is wrong.

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The top one has them in reverse alphabetical order, your selected species list is in alphabetical order.

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Cross-posted on bioinfo SE (H/T bioinfo SE user gringer): https://bioinformatics.stackexchange.com/questions/20139/manually-order-the-set-fails-in-upsetr

OP, don't post in multiple forums, it's bad etiquette.

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