seurat::key in RunHarmony results in an error

[DivyaRavichandar]

Running the RunHarmony(seuratobject) with seurat 4.0.3 results in the following error

  no applicable method for 'Key' applied to an object of class "character"```

The issue seems to stem from this one line of code in RunHarmony.R that was recently added
`reduction.key <- Seurat::Key(reduction.save, quiet = TRUE)`

Is this edit backward compatible with older Seurat versions?

[HenriettaHolze]

I get the same error

Error in UseMethod(generic = "Key", object = object) : 
  no applicable method for 'Key' applied to an object of class "character"

I use Seurat 4.1.0 and Harmony 0.1.1., R v4.1.0

[ecdabe-BISC]

Ditto with R version 4.0.4 Harmony 0.1.1

[hghaoo]

i met the same problem, and get resolved by Harmony 0.1.0.

[longerping1992]

I met the same problem.

InstallData("pbmcsca")
data("pbmcsca")
pbmcsca <- NormalizeData(pbmcsca) %>% FindVariableFeatures() %>% ScaleData() %>% RunPCA(verbose = FALSE)
pbmcsca <- RunHarmony(pbmcsca, group.by.vars = "Method")
Harmony 9/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony converged after 9 iterations
Error in UseMethod(generic = "Key", object = object) :
no applicable method for 'Key' applied to an object of class "character"

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/local/intel/compilers_and_libraries_2020.2.254/linux/mkl/lib/intel64_lin/libmkl_rt.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] pbmcsca.SeuratData_3.0.0 harmony_0.1.1 Rcpp_1.0.8
[4] SeuratData_0.2.2 SeuratObject_4.0.4 Seurat_4.1.0

loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_2.0-2 deldir_0.2-10
[4] ellipsis_0.3.2 ggridges_0.5.3 rprojroot_2.0.2
[7] fs_1.5.2 spatstat.data_2.1-0 leiden_0.3.8
[10] listenv_0.8.0 remotes_2.4.2 ggrepel_0.9.1
[13] fansi_1.0.3 codetools_0.2-18 splines_4.0.5
[16] cachem_1.0.6 polyclip_1.10-0 pkgload_1.3.2
[19] jsonlite_1.7.3 ica_1.0-2 cluster_2.1.2
[22] png_0.1-7 uwot_0.1.10 shiny_1.6.0
[25] sctransform_0.3.3 spatstat.sparse_2.0-0 compiler_4.0.5
[28] httr_1.4.2 assertthat_0.2.1 Matrix_1.3-4
[31] fastmap_1.1.0 lazyeval_0.2.2 cli_3.1.1
[34] later_1.2.0 htmltools_0.5.2 prettyunits_1.1.1
[37] tools_4.0.5 igraph_1.3.2 gtable_0.3.0
[40] glue_1.6.2 RANN_2.6.1 reshape2_1.4.4
[43] dplyr_1.0.9 rappdirs_0.3.3 scattermore_0.7
[46] vctrs_0.4.1 nlme_3.1-152 lmtest_0.9-38
[49] stringr_1.4.0 globals_0.14.0 ps_1.6.0
[52] mime_0.11 miniUI_0.1.1.1 lifecycle_1.0.1
[55] irlba_2.3.5 devtools_2.4.3 goftest_1.2-2
[58] future_1.21.0 MASS_7.3-54 zoo_1.8-9
[61] scales_1.1.1 spatstat.core_2.2-0 promises_1.2.0.1
[64] spatstat.utils_2.2-0 parallel_4.0.5 RColorBrewer_1.1-2
[67] curl_4.3.2 memoise_2.0.1 reticulate_1.24
[70] pbapply_1.4-3 gridExtra_2.3 ggplot2_3.3.5
[73] rpart_4.1-15 stringi_1.7.6 pkgbuild_1.3.1
[76] rlang_1.0.4 pkgconfig_2.0.3 matrixStats_0.62.0
[79] lattice_0.20-44 ROCR_1.0-11 purrr_0.3.4
[82] tensor_1.5 patchwork_1.1.1 htmlwidgets_1.5.4
[85] cowplot_1.1.1 tidyselect_1.1.2 processx_3.5.2
[88] parallelly_1.26.1 RcppAnnoy_0.0.18 plyr_1.8.6
[91] magrittr_2.0.2 R6_2.5.1 generics_0.1.2
[94] DBI_1.1.1 withr_2.5.0 pillar_1.7.0
[97] mgcv_1.8-36 fitdistrplus_1.1-5 survival_3.2-11
[100] abind_1.4-5 tibble_3.1.7 future.apply_1.7.0
[103] crayon_1.5.2 KernSmooth_2.23-20 utf8_1.2.2
[106] spatstat.geom_2.2-0 plotly_4.9.4.1 usethis_2.1.6
[109] grid_4.0.5 data.table_1.14.2 callr_3.7.0
[112] digest_0.6.29 xtable_1.8-4 tidyr_1.1.3
[115] httpuv_1.6.1 munsell_0.5.0 viridisLite_0.4.0
[118] sessioninfo_1.2.2

[longerping1992]

Hi all, I addressed it by following this #170.
Specifically, I downloaded the harmony-master.zip from https://github.com/immunogenomics/harmony.
Unzip it. In "RunHarmony.R", remove "reduction.key <- Seurat::Key(reduction.save, quite = TRUE", add "reduction.key = reduction.save".
Then install using "devtools::install_local('/gpfs/gsfs12/users/longe2/Software/harmony-master/')". If you do not have devtool, install devtool first.
Restart the R, and it works.

[pati-ni]

I think there was some bug in Seurat::Key that resulted in this error. Latest Seurat 4.4.0 and Seurat v5 do not fail with this. Closing for now, feel free to re-open if there are any issues

[pati-ni]

Linking this reference this:
satijalab/seurat#6533 (comment)

Despite not dealing with the error offended line is not failing with latest Seurat versions