NA group appears in group drawing about immunarch

[moyangpei]

In addition, many detailed parameters of this package are not listed, and the drawings can not be modified. Can you provide a more detailed manual? Thank you very much.

[vadimnazarov]

Hi, thank you for noticing that! Can you please send me your metadata file? Email: vdm.nazarov at gmail com

Drawing can be modified by using fixVis, see here: https://immunarch.com/articles/7_fixvis.html

Can you please provide a list where you want to modify drawing, but you can't?

The package is not released, it's in under active development, so many features and documentation parts can be missed. It would be a great help for you is you provide us a list of issues and missing documentation that you want to improve.

[moyangpei]

Hi, I have sent the metadata file to you a few days ago and look forward to your reply.Thank you very much.

[vadimnazarov]

Working on it! The issue you described is much harder than we expected, so it takes more time than usual to fix it.

[veronicanoyaro]

Hi

i am having a similar problem
when using this code

p6 = vis(imm_topTCRd, .by= "ELISA", .meta= TCRd$meta)
p6

#ELISA is one of the columns in my metadata.txt file contains NEG/POS/
I am not being able to actually group the samples. i have 30 aprox samples and they are all plotted in each top clonal proportion x value without assigning any of the to a NEG/POS ELISA group ,

the plot i get would be something like this
/home/veronicanoyaro/Documents/PASTEUR/TCRCLONOTYPES/ANALYSIS/IMMUNARCH/TCRD/Rplot01.png

I have also tryed to pass it as a vector like this

by_vec_ELISA = TCRd$meta$ELISA

p6 = vis(imm_topTCRd, .by= by_vector_ELISA, .meta= TNA)
and i get the following message

Warning messages:
1: Unknown or uninitialised column: 'p'.
2: Computation failed in stat_compare_means():
argument "x" is missing, with no default

i have just downloaded the last version but it remains 0.4.0
I really appreciate any help
Faithfully

[vadimnazarov]

Hi everyone,

this issue appears much more complicated that we first anticipated it and we can't reproduce it.

@moyangpei can you please send me the code that you used to generate such plots?

@veronicanoyaro can you please send us both the code and the metadata that you used to generate such plots?

Thank you! Looking forward to your responses.

[vadimnazarov]

Thank you for sending us the code and the data! Can you please update the package to the latest 0.5.4 version and try it again?

[veronicanoyaro]

Sure! Thank you very much! El mié., 4 dic. 2019 a las 11:07, Vadim Nazarov (<[email protected]>) escribió:

…

Thank you for sending us the code and the data! Can you please update the package to the latest 0.5.4 version and try it again? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#7?email_source=notifications&email_token=AMK3ONQI5D4N2QAMPTSPSHDQW62TLA5CNFSM4H4SRGO2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEF5EGMI#issuecomment-561660721>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMK3ONQMOWDCOLS4VFZ7VRLQW62TLANCNFSM4H4SRGOQ> .

[EugeneRumynskiy]

@moyangpei @veronicanoyaro How it's going? I'am closing the issue. If you have any questions or unresolved problems please let us know here. If any it's possible to reopen this issue or create a new one.