Question: Creating a 5-way Venn diagram
0
gravatar for Stef
9 months ago by
Stef0
Stef0 wrote:

Hello,

I want to create a Venn diagram.

I am trying to use the overLapper function.

I created six CSV files with DEGs for six tissues (pollen, 1 week old bagged flowers, 1 week old unbagged flowers, recently open flowers, one month old seed capsule, three month old seed capsule).

I made lists of characters for each tissue. For some overLapper won't accept my list. I always get this error:

Error in overLapper(SetList, type = "vennsets") : Unexpected input. The input 'setlist' needs to be of class 'list' where each list component stores a label set as 'vector' and the name of each label set is provided under the name slot of each list component.

Here is my code:

BiocManager::install("systemPipeR")

library(systemPipeR)

EF <- as.character(read.csv("DEGslist_EF.csv", header = F, sep = ",")$V1)
LFB <- as.character(read.csv("DEGslist_LFB.csv", header = F, sep = ",")$V1)
LFU <- as.character(read.csv("DEGslist_LFU.csv", header = F, sep = ",")$V1)
EC <- as.character(read.csv("DEGslist_EC.csv", header = F, sep = ",")$V1)
LC <- as.character(read.csv("DEGslist_LC.csv", header = F, sep = ",")$V1)

setlist <- list(EF, LFB, LFU, EC, LC)

vennset <- overLapper(setlist, type="vennsets")
vennPlot(vennset)

Thanks!

rna-seq R • 199 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by Stef0
1
  1. setlist is not the same as SetList. What is the actual variable name?
  2. What is the output of names(setlist)?
ADD REPLYlink written 9 months ago by RamRS30k

Sorry.

  1. They are the same thing. I just edited it.
  2. The output is "NULL". What does that mean?
ADD REPLYlink written 9 months ago by Stef0
1
gravatar for jared.andrews07
9 months ago by
jared.andrews077.6k
Memphis, TN
jared.andrews077.6k wrote:

It means your list isn't named, and it needs to be. Try setlist <- list("EF" = EF, "LFB" = LFB, "LFU" = LFU, "EC" = EC, "LC" = LC).

ADD COMMENTlink written 9 months ago by jared.andrews077.6k

IT WORKED!!!!

Thank you :)

ADD REPLYlink written 9 months ago by Stef0

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work.

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ADD REPLYlink written 9 months ago by RamRS30k
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