baderlab / humanliver Goto Github PK

Hello,

I recently updated my R packages, in particular the scClustViz from v0.5.2 (I think) to v1.0.0. Now after loading the HumanLiver package and running viewHumanLiver(), I get the following error:

Error in FUN(X[[i]], ...) : Unexpected input object.
In addition: Warning messages:
1: replacing previous import ‘BiocGenerics::dims’ by ‘Biobase::dims’ when loading ‘AnnotationDbi’
2: In if (is(get(lfc[X])[[1]]) == "sCVdata") { :
the condition has length > 1 and only the first element will be used

Any idea what could cause this?

Thank you for your help in advance,
Juliane

My sessionInfo output:

R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] Matrix_1.2-8 org.Hs.eg.db_3.7.0 AnnotationDbi_1.44.0 IRanges_2.16.0
[5] S4Vectors_0.20.1 Biobase_2.40.0 BiocGenerics_0.28.0 HumanLiver_1.2.0

loaded via a namespace (and not attached):
[1] tidyselect_0.2.5 remotes_2.0.2 purrr_0.3.0 lattice_0.20-34 colorspace_1.4-0
[6] testthat_1.0.2 viridisLite_0.3.0 usethis_1.4.0 htmltools_0.3.6 blob_1.1.1
[11] rlang_0.3.1 pkgbuild_1.0.2 pillar_1.3.1 later_0.8.0 glue_1.3.0
[16] withr_2.1.2 DBI_1.0.0 bit64_0.9-5 bindrcpp_0.2.2 sessioninfo_1.1.1
[21] bindr_0.1.1 plyr_1.8.4 munsell_0.5.0 gtable_0.2.0 devtools_2.0.1
[26] memoise_1.0.0 callr_3.1.1 httpuv_1.4.5.1 ps_1.3.0 curl_3.3
[31] Rcpp_1.0.0 xtable_1.8-3 backports_1.1.3 promises_1.0.1 scales_1.0.0
[36] desc_1.2.0 pkgload_1.0.2 mime_0.6 fs_1.2.6 bit_1.1-14
[41] gridExtra_2.3 ggplot2_3.1.0 digest_0.6.18 dplyr_0.7.8 processx_3.2.1
[46] shiny_1.2.0 rprojroot_1.2 grid_3.5.0 cli_1.0.1 tools_3.5.0
[51] magrittr_1.5 tibble_2.0.1 lazyeval_0.2.1 RSQLite_2.1.1 crayon_1.3.4
[56] pkgconfig_2.0.2 scClustViz_1.0.0 prettyunits_1.0.2 assertthat_0.2.0 rstudioapi_0.9.0
[61] viridis_0.5.1 R6_2.4.0 compiler_3.5.0

Hi,
I want to know the unit of the data you provided in HuamanLiverSeurat@data so I can run some downstream analysis of my own. Is it log2(TPM + 1) and is it scaled somehow?
Thx.

Hello

Firstly, I'd like to thank you for publishing the valuable scRNA seq dataset.

Could you give me advice on identifying the name of cell-types from the Rdata file?

I can see that load("data/HumanLiver/inst/liver/HumanLiver.RData") loads two variables, HumanLiverSeurat and sCVdL, into workspace.

And I found gene-cell matrix is in HumanLiverSeurat[['RNA']]@data( in case of raw count, HumanLiverSeurat[['RNA']]@counts)

I guess that cluster(or cell type) information is in [email protected](or [email protected]$res.0.8, which is the same as it) as the number of unique values is 20, which is in line with that of publication.
However, I failed to identify to which cell-types each integer in active.ident column corresponds.
(ex.endothelial cells, cholangiocytes, hepatic stellate cells, B cells, etc.)

Could you help me out with this? Am I missing something?
Thank you for your help in advance,

Best regards,
Chanwoo Kim

Dear all,

I am having issues to install the "HumanLiver" package.
I am running the newest version of R (4.0.0) on MacOS and all the packages are also updated.

`> devtools::install_github("BaderLab/HumanLiver")
Downloading GitHub repo BaderLab/HumanLiver@master
✓ checking for file ‘/private/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T/Rtmp3cE6pF/remotes10e17b3a97b/BaderLab-HumanLiver-39c873b/DESCRIPTION’ ...
─ preparing ‘HumanLiver’:
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: ‘HumanLiver/inst/liver/HumanLiver.RData’
─ building ‘HumanLiver_1.5.0.tar.gz’

• installing source package ‘HumanLiver’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  sh: line 1: 4621 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T//RtmpcNy9lM/file120675b2df47'
  ERROR: lazy loading failed for package ‘HumanLiver’
• removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/HumanLiver’
  installation of package ‘/var/folders/yn/tbw3r2xn0m94qrwvh1h16mnw0000gn/T//Rtmp3cE6pF/file10e1243bce30/HumanLiver_1.5.0.tar.gz’ had non-zero exit status`

As you can see the installation fails and I am not sure why. Do you have an idea what the problem could be?

Thank you.
Best regards,
E. Viho