UpSet: Error in start_col:end_col : argument of length 0

Question

[Jonas.Koch]

Hi!

I processed 3 BAM files that were generated from 3 different pipelines, so in total 9 BAM files by writing scripts in bash and python. I extracted the mapped reads from the BAM files and stored them in python sets. Then, I performed pair-wise intersection operations to see which reads are common in which BAM files (despite different pipelines).

The output 3x3 matrix was written into a tsv file:

14659   14659   14647
14659   15731   15709
14647   15709   15709

Numbers correspond to the number of reads that are in one intersection between 2 files.

Now, I wanted to load the marix into R and create an UpSet R plot. I know that a Venn Diagram would also work, but later on, I will have more pipelines to compare and so I chose UpSet R plots. I tried this code:

upset(test_df, sets = 'reconstructed', 'shuffled', 'trimmed',
      number.angles = 30, point.size = 3.5, line.size = 2, 
      mainbar.y.label = "Read Intersections", sets.x.label = "Blabla", 
      text.scale = c(1.3, 1.3, 1, 1, 2, 0.75), mb.ratio = c(0.55, 0.45),
      order.by = 'sets', keep.order = TRUE)

But an error occured:
Error in start_col:end_col : argument of length 0

Unfortunately, I am only a beginner in R w/o experience. Maybe, someone has more experience in R or the UpSet package.

Greetings!

[Jeremy Leipzig]

i think you should have a dataframe that is 15731 rows in length (one for each read), and four columns (one read name and three logical true/false columns for being a member of that file)

[GenoMax]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

Answer 1

[Friederike]

what does test_df look like? Can you post the result of head(test_df)?

It seems to me like the sets parameter should be a vector, i.e. sets = c("reconstructed","shuffled",trimmed"), but it's difficult to test without know what test_df looks like.