saezlab
Unable to aggregate Cell Chat output
I generated liana result from my single-cell dataset. However, I was unable to aggregate the CCC results if I included the cell chat output
The command used to generate liana result:
liana_res <- liana_wrap(sc_res, c('call_cellchat', "natmi", "connectome", "logfc", "sca", "cellphonedb"),idents_col ="final_cell_type")
Error Message:
> tmp <- liana_res %>% liana_aggregate()
Now aggregating call_cellchat
Now aggregating natmi
Now aggregating connectome
Now aggregating logfc
Now aggregating sca
Now aggregating cellphonedb
Aggregating Ranks
Error in `.rowNamesDF<-`(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning messages:
1: In exec(output, ...) :
Using internal and external methods should be done with caution!
2: non-unique values when setting 'row.names': ‘B1_B2⊎B1_B2⊎AMH⊎AMHR2’, ‘B1_B2⊎B1_B2⊎BMP2⊎BMPR1A’, ‘B1_B2⊎B1_B2⊎BMP2⊎BMPR1B’, ‘B1_B2⊎B1_B2⊎BMP2⊎BMPR2’, ‘B1_B2⊎B1_B2⊎BMP4⊎BMPR1A’, ‘B1_B2⊎B1_B2⊎BMP4⊎BMPR1B’, ‘B1_B2⊎B1_B2⊎BMP4⊎BMPR2’, ‘B1_B2⊎B1_B2⊎BMP6⊎ACVR1’, ‘B1_B2⊎B1_B2⊎BMP6⊎BMPR1A’, ‘B1_B2⊎B1_B2⊎BMP6⊎BMPR1B’, ‘B1_B2⊎B1_B2⊎BMP6⊎BMPR2’, ‘B1_B2⊎B1_B2⊎BMP7⊎ACVR1’, ‘B1_B2⊎B1_B2⊎BMP7⊎BMPR1A’, ‘B1_B2⊎B1_B2⊎BMP7⊎BMPR1B’, ‘B1_B2⊎B1_B2⊎BMP7⊎BMPR2’, ‘B1_B2⊎B1_B2⊎BMP8A⊎ACVR1’, ‘B1_B2⊎B1_B2⊎BMP8A⊎BMPR1A’, ‘B1_B2⊎B1_B2⊎BMP8A⊎BMPR1B’, ‘B1_B2⊎B1_B2⊎BMP8A⊎BMPR2’, ‘B1_B2⊎B1_B2⊎FN1⊎ITGAV’, ‘B1_B2⊎B1_B2⊎FN1⊎ITGB1’, ‘B1_B2⊎B1_B2⊎GDF11⊎ACVR1B’, ‘B1_B2⊎B1_B2⊎GDF3⊎ACVR1B’, ‘B1_B2⊎B1_B2⊎GDF3⊎ACVR1C’, ‘B1_B2⊎B1_B2⊎GDF9⊎BMPR2’, ‘B1_B2⊎B1_B2⊎LAMA1⊎ITGB1’, ‘B [... truncated]
This is the screenshot for the cellchat result ( it seems that it missed several columns that are found in other CCC output)
Hi,
This is likely related to perhaps using CellChatv2? I tried the latest version from the now archived CellChatv1 with which liana was designed to work with and it worked well.
Please try installing CellChat from https://github.com/sqjin/CellChat, and let me know if this works.
Hi Daniel, thank you so much for your time! I tried 1.0.0 and 1.5.0, both yielded the same error msg as sfpacman indicated above. I attached a preview of what the liana_test object looks like if that helps, and would be willing to provide other info. Thanks again.
@SChao58 I ran into the exact same issue at liana_aggregate() step.
Initially I ran liana_wrap() with all 12 available methods, but 6 of them gave something called purrr_error, so I removed them from the result list and ran liana_aggregate() with the remaining 6, the same as your screenshot. Then I also got:
Error in `.rowNamesDF<-`(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning messages:
1: In exec(output, ...) :
Using internal and external methods should be done with caution!
2: non-unique values when setting 'row.names': ‘Astro⊎Astro⊎Bmp6⊎Acvr2a’, ‘Astro⊎Astro⊎Bmp6⊎Acvr2b’, ‘Astro⊎Astro⊎Bmp6⊎Bmpr2’, ‘Astro⊎Astro⊎Tgfb2⊎Acvr1’,
I feel quite stuck.. Should I try the python version of Liana instead?
