My venn diagrams dont intersect - what's missing/wrong with my code

Question

I have two lists of genes and i want to represent the overlap between the lists in a venn diagram. Could anybody suggest what I am missing in the code below? I'm using the VennDiagram package and the result i get is two non intersecting circles. I have also used Venny https://bioinfogp.cnb.csic.es/tools/venny/index2.0.2.html to draw the venn and confirmed there is an overlap.

library(VennDiagram)

#select the data
dataset1 <- data.frame(as.character(v7$HGNC_Symbol)) #567 genes
dataset2 <- data.frame(as.character(test$toupper.v13.HGNC_Symbol.)) #476 genes

#rename the columns so I know the source
names(dataset1)[1] <- "Progenesis"
names(dataset2)[1] <- "BiomaRt"

#sort the dataframes alphabetically 
dataset1 <- dataset1 %>% arrange(Progenesis)
dataset2 <- dataset2 %>% arrange(BiomaRt)

#create a list of numbers and join it to dataframe1
mylist <- c(1:592)
dataset1 <- data.frame(mylist, dataset1)

#create a list of numbers and join it to dataframe2
mylist <- c(1:494)
dataset2 <- data.frame(mylist, dataset2)

#join the two dataframes
v <- plyr::join(dataset1, dataset2, type='full')

#draw the Venn Diagram

Dataset1 <- as.vector(v$Progenesis)
Dataset2 <- as.vector(v$BiomaRt)
Dataset2 <- na.omit(Dataset2)

    #first 20 rows of each dataset 
    dput(Dataset1)
        c("AACS ", "AARS ", "ABCF1 ", "ACAD11 ", "ACIN1 ", "ACO1 ", "ACOX3 ", 
        "ACP1 ", "ACSL3 ", "ACY1A ", "ACYP1 ", "ADA ", "ADI1 ", "ADK ", 
        "ADSL ", "ADSS ", "AGPAT3 ", "AHSA2 ", "AK4 ", "AKAP1 ")
        dput(Dataset2)
        structure(c("AACS", "AARS", "AARS", "ABCF1", "ACAD11", "ACIN1", 
        "ACO1", "ACOX3", "ACSL3", "ACYP1", "ADA", "ADI1", "ADK", "ADSL", 
        "AGPAT3", "AHSA2", "AKAP1", "AKAP12", "AKR1A1", "AKR1A1"),
        na.action = structure(495:592, class = "omit"))

venn.diagram(
  x = list(Dataset1, Dataset2),
  category.names = c("Set1" , "Set2"),
  filename = 'venn_diagram.png',
  output=TRUE
  )

All suggestions welcome.

Thanks

The result of my code is this

What I want is here

Hi there. Just a hint: Instead of `c(seq(1:494))` you can use `1:494`. Since `list` is the name of a datatype and a function it's usally better to use other names like `my_list`. Is it possible to show us some example data? — Martin Gal, Apr 30 '20 at 22:48
Hi Martin. Thanks for the suggestions. Have made those changes. If you need the datsets whats the best way of attaching them? — Peadar, May 01 '20 at 09:59
Please share (part of) your data https://stackoverflow.com/questions/49994249/example-of-using-dput — desval, May 01 '20 at 10:32

score 0 · Accepted Answer · answered May 01 '20 at 23:24

I have a few remarks on your data:

dput(Dataset1)
        c("AACS ", "AARS ", "ABCF1 ", "ACAD11 ", "ACIN1 ", "ACO1 ", "ACOX3 ", 
        "ACP1 ", "ACSL3 ", "ACY1A ", "ACYP1 ", "ADA ", "ADI1 ", "ADK ", 
        "ADSL ", "ADSS ", "AGPAT3 ", "AHSA2 ", "AK4 ", "AKAP1 ")
dput(Dataset2)
        structure(c("AACS", "AARS", "AARS", "ABCF1", "ACAD11", "ACIN1", 
        "ACO1", "ACOX3", "ACSL3", "ACYP1", "ADA", "ADI1", "ADK", "ADSL", 
        "AGPAT3", "AHSA2", "AKAP1", "AKAP12", "AKR1A1", "AKR1A1"),
        na.action = structure(495:592, class = "omit"))

Your Dataset1 contains strings ending with a whitespace. They are not equal to the ones in Dataset2, for example "AACS " is not the same as "AACS". Try transforming your dataset to

Dataset1 <- c("AACS","AARS","ABCF1","ACAD11","ACIN1","ACO1","ACOX3", 
              "ACP1","ACSL3","ACY1A","ACYP1","ADA","ADI1","ADK", 
              "ADSL","ADSS","AGPAT3","AHSA2","AK4","AKAP1")

In this case your output should look like this: Your output filetyp is .png, therefor you should use the parameter imagetype='png'.

Hi @Martin Gal. Thanks for that help. Could you advise how I do that transformation? I am new to this and haven't quite gotten my head around transforming data. — Peadar, May 05 '20 at 20:12
Suppose your dataset is named `Dataset1` and there are spaces at the end like shown above. In this case you could use `gsub("[[:space:]]$", "", Dataset1)`. `gsub` uses regular expressions and looks for a pattern, in this case *spaces* `[[:space:]]` at the end `$`. These are replaced by an empty string "". Note: If there are more transformations needed, this special transformation won't help you. And if this answer was helpful feel free to accept it. :-) — Martin Gal, May 05 '20 at 20:37

My venn diagrams dont intersect - what's missing/wrong with my code

1 Answers1