Errors running antibody forests vignette

[duinsel]

Hi,

I tried running the antibody forests vignette on several systems. With the CRAN version of Platypus, the datasets load OK, but all subsequent analysis with the AntibodyForests function throws an error

AntibodyForests(VGM[[1]], network.algorithm = 'tree', specific.networks = 'clonotype7') %>% AntibodyForests_plot(node.label = NULL, node.scale.factor = 8) Error in assign(mname, def, where) : cannot add bindings to a locked environment

I saw this on several systems (Win/linux), including a fresh install.

I performed a Github install of Platypus instead. Fortunately, I can generate the plots on VDJ data in this way, but that install generates another error when loading the GEX data

`PlatypusDB_fetch(PlatypusDB.links = c("agrafiotis2021a/TNFR2.BM.3m.S1/ALL"), load.to.enviroment = T, combine.objects = T) 2022-10-02 09:32:03: Starting download of agrafiotis2021a_TNFR2.BM.3m.S1_VDJ.RData... 2022-10-02 09:32:04: Starting download of agrafiotis2021a_TNFR2.BM.3m.S1_GEX.RData... [1] "agrafiotis2021a_TNFR2.BM.3m.S1_VDJGEXdata"

VGM <- VDJ_GEX_matrix(Data.in = list(agrafiotis2021a_TNFR2.BM.3m.S1_VDJGEXdata), parallel.processing = "parlapply", trim.and.align = T) 09:32:29 Loading in data 09:32:29 Loaded VDJ data from Data.in

Loading GEX failed object 'directory_read10x' not found Getting VDJ GEX stats Starting with 1 of 1 Getting 10x stats 09:32:32 Got VDJ GEX stats `

Is there a way to circumvent either error, or to get the best of both worlds between CRAN and github versions?

Thanks!

[vickreiner]

Hi, Thanks for noting this! We have pushed some new features and bugfixes which have not made it to CRAN yet. We plan to push the next version to CRAN this week to sync it up.

Concerning the VDJ GEX matrix, I did push a fix, so that problem should now be solved in the Git install.

[EdGreen21]

can confirm that pulling latest version from github fixes this