formatting issue in data for Upset plots

Question

[gfreimanis]

Sorry, this is my first post so apologise if i miss details, but I am trying to use UpSetR to plot some data of different variants, however I cannot get the data in the correct format to produce the graphs. I keep getting the following errors:

Error in start_col:end_col : argument of length 0

file("") only supports open = "w+" and open = "w+b": using the former

I have tried to insert the data via a number of formats ranging from excel to different variations of .csv trying to match the toy datasets i.e. movies, etc but cannot get it to work.

Would you please be able to take a quick look and let me know where my formatting is going wrong? The commands have included the below:

upset(Knew, sets = c("EP25", "EP50", "EP60", "EP65", "EP75", "EP85", "EP95", EP100", "Vaccine"), number.angles = 30, point.size = 3.5, line.size = 2, mainbar.y.label = "No.Variants", sets.x.label = "Lineages", order.by = "sets", keep.order = "TRUE")

Knew.csv:
"Genome_location","EP25","EP50","EP60","EP65","EP75","EP85","EP95","EP100","Vaccine"
"40" ,"1","0","0","0","0","0","0","0","0"
"140" ,"0","0","0","0","0","1","1","1","1"
"319" ,"0","0","0","0","0","1","1","1","1"
"572" ,"1","1","1","1","1","1","1","1","1"
"573" ,"0","0","0","0","1","0","0","1","0"
"575" ,"0","0","1","1","1","0","1","1","0"
"585" ,"0","0","0","1","1","0","1","0","0"
"610" ,"0","0","0","0","0","1","1","1","1"
"706" ,"0","1","1","1","1","0","1","0","0"
"750" ,"0","1","1","1","1","0","1","1","0"
"809" ,"0","0","0","0","0","0","1","1","0"

[gfreimanis]

Hi swbarnes2,

thanks for the comment. I have amended the example above to reflect what i have tried so far. I have also been putting in as an excel sheet but it made no difference.

I tried to delete genome location from the first header box but it did not make a difference.

Thanks

Answer 1

[swbarnes2]

Why don't your sets names match anything in the csv?

I'd see if nsets works instead. ID's also try removing "Genome_location", and just having that be blank instead. R is generally happier with row names don't have a column header.