Comments (11)
That depends on how to explain the field which contains the 0/NA values. A preprocessing step of filtering out 0/NA values before plotting by ggvenn would help if required.
By the way, could you provide an example to make the issue clearer?
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Hello,
I am having the same problem - I have three columns but two are shorter than the other so end up having blank cells at the end of their last values - therefore these are appearing as common values between the two groups. I have tried to delete these cells prior to uploading to R but this hasn't worked.
I am not sure how to make an example for you but it was uploaded as a csv - sorry if that isn't enough info!
Thanks,
Amy
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Hi, @amy-houseman
If you have loaded the csv into R as variable 'a', you can try dput(a)
to get the construction command. If the file is too big, I suggest you simplify it first. We just need a minimal case to show the problem.
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Hi,
Thanks for you reply! I managed to fix my problem with
df[df == ''] <- NA
df <- na.omit(df)
Before turning it into a list for ggvenn! Thank you :))
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Thank you very much for the useful sharing. I think I can close this issue now.
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Hello,
Sorry, me again! I was able to use df[df == ''] <- NA
to add na to the blanks but actually df <- na.omit(df) was removing the entire row from being used in the Venn diagram.
csv file uploaded = TEST_overlapping_GOF_LOF_2_plus_denovo
Code:
a <- TEST_overlapping_GOF_LOF_2_plus_denovo
a[a == ''] <- NA
a <- na.omit(a)
library(ggvenn)
a <- list('LOF_2_or_more_list'= a$LOF_2_or_more_list,
'GOF_2_or_more_list' = a$GOF_2_or_more_list,
'De_novo' = a$De_novo)
ggvenn(a, c("LOF_2_or_more_list", "GOF_2_or_more_list", "De_novo"), fill_color = c("pink", "lightblue3", "mediumseagreen"))
I tired to dput(a) but I think it misses out the end of the file which is where the problems occur - I have made a small version of the file attached
TEST_overlapping_GOF_LOF_2_plus_denovo.csv
To produce the venn:
a <- TEST_overlapping_GOF_LOF_2_plus_denovo
library(ggvenn)
a <- list('LOF_2_or_more_list'= a$LOF_2_or_more_list,
'GOF_2_or_more_list' = a$GOF_2_or_more_list,
'De_novo' = a$De_novo)
ggvenn(a, c("LOF_2_or_more_list", "GOF_2_or_more_list", "De_novo"), fill_color = c("pink", "lightblue3", "mediumseagreen"))
As you can see from this example, there should be:
LOF_2_or_more_list Vs De_novo = 3 overlaps (A,B,C).
LOF_2_or_more_list should have 2 of its own values (D,E).
and GOF_2_or_more_list should not overlap with anything but have 1 of its own values (H).
But as you can see:
LOF_2_or_more_list Vs De_novo = 3
LOF_2_or_more_list = 2 own values
GOF_2_or_more_list = 1 of its own
GOF_2_or_more_list Vs De_novo = 1
This GOF_2_or_more_list Vs De_novo = 1 is caused by the GOF_2_or_more_list and De_novo list both having blank cells which are being detected as shared values.
Do you know what can stop these blanks being detected as values?
Thanks!
Amy
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Yes, you're right. NA should not be counted in such cases. That is indeed a bug. I will fix it soon.
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Hi, @amy-houseman
I have fixed this issue in this commit, and published a new release (v0.1.10), as well as on CRAN.
You may upgrade to the new version by either
devtools::install_github("yanlinlin82/ggvenn")
or
install.package("ggvenn")
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Hi, I have installed the new version but I'm still not sure its working - could I send you my file via email for you to test? Thanks! Sorry to be a pain! Amy
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Hi, I have installed the new version but I'm still not sure its working - could I send you my file via email for you to test? Thanks! Sorry to be a pain! Amy
ok
from ggvenn.
Hello @yanlinlin82 ,
Thank you for updating the package,
I will test again soon,
Sorry, but I believe I missed the updates for this discussion,
Best Regards,
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