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immunogenomics
Error in `dplyr::select()`: ! <text>:1:5: unexpected symbol
Hi,
I am getting the following error when I run RunHarmony on my Seurat object and I can't work out where this dplyr::select() is coming from.
seurat_object <- RunHarmony(seurat_object, group.by.vars = "donor")
Error in
dplyr::select(): ! <text>:1:5: unexpected symbol 1: Use of ^ Runrlang::last_error()to see where the error occurred.
rlang::last_error()
<simpleError in dplyr::select(., -.data$row_id):
:1:5: unexpected symbol 1: Use of ^
Best wishes, Lucy
sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /Filers/package/R-base/4.2.0/lib64/R/lib/libRblas.so
LAPACK: /Filers/package/R-base/4.2.0/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] harmony_0.1.0 Rcpp_1.0.9 patchwork_1.1.2
[4] forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10
[7] purrr_0.3.5 readr_2.1.3 tidyr_1.2.1
[10] tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.2
[13] sp_1.5-0 SeuratObject_4.1.2 Seurat_4.2.0
loaded via a namespace (and not attached):
[1] readxl_1.4.1 backports_1.4.1 plyr_1.8.7
[4] igraph_1.3.5 lazyeval_0.2.2 splines_4.2.0
[7] listenv_0.8.0 scattermore_0.8 digest_0.6.29
[10] htmltools_0.5.3 fansi_1.0.3 magrittr_2.0.3
[13] tensor_1.5 googlesheets4_1.0.1 cluster_2.1.4
[16] ROCR_1.0-11 tzdb_0.3.0 globals_0.16.1
[19] modelr_0.1.9 matrixStats_0.62.0 spatstat.sparse_2.1-1
[22] colorspace_2.0-3 rvest_1.0.3 ggrepel_0.9.1
[25] haven_2.5.1 xfun_0.30 crayon_1.5.2
[28] jsonlite_1.8.2 progressr_0.11.0 spatstat.data_2.2-0
[31] survival_3.4-0 zoo_1.8-11 glue_1.6.2
[34] polyclip_1.10-0 gtable_0.3.1 gargle_1.2.1
[37] leiden_0.4.3 future.apply_1.9.1 abind_1.4-5
[40] scales_1.2.1 DBI_1.1.3 spatstat.random_2.2-0
[43] miniUI_0.1.1.1 viridisLite_0.4.1 xtable_1.8-4
[46] reticulate_1.26 spatstat.core_2.4-4 htmlwidgets_1.5.4
[49] httr_1.4.4 RColorBrewer_1.1-3 ellipsis_0.3.2
[52] ica_1.0-3 pkgconfig_2.0.3 farver_2.1.1
[55] uwot_0.1.14 dbplyr_2.2.1 deldir_1.0-6
[58] utf8_1.2.2 tidyselect_1.2.0 labeling_0.4.2
[61] rlang_1.0.5 reshape2_1.4.4 later_1.3.0
[64] munsell_0.5.0 cellranger_1.1.0 tools_4.2.0
[67] cli_3.4.1 generics_0.1.3 broom_1.0.1
[70] ggridges_0.5.4 evaluate_0.17 fastmap_1.1.0
[73] yaml_2.3.5 goftest_1.2-3 knitr_1.40
[76] fs_1.5.2 fitdistrplus_1.1-8 RANN_2.6.1
[79] pbapply_1.5-0 future_1.28.0 nlme_3.1-160
[82] mime_0.12 ggrastr_1.0.1 xml2_1.3.3
[85] compiler_4.2.0 rstudioapi_0.14 beeswarm_0.4.0
[88] plotly_4.10.0 png_0.1-7 spatstat.utils_2.3-1
[91] reprex_2.0.2 stringi_1.7.8 rgeos_0.5-9
[94] lattice_0.20-45 Matrix_1.5-1 vctrs_0.4.2
[97] pillar_1.8.1 lifecycle_1.0.1 spatstat.geom_2.4-0
[100] lmtest_0.9-40 RcppAnnoy_0.0.19 data.table_1.14.2
[103] cowplot_1.1.1 irlba_2.3.5.1 httpuv_1.6.6
[106] R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20
[109] gridExtra_2.3 vipor_0.4.5 parallelly_1.32.1
[112] codetools_0.2-18 MASS_7.3-58.1 assertthat_0.2.1
[115] withr_2.5.0 sctransform_0.3.5 mgcv_1.8-40
[118] parallel_4.2.0 hms_1.1.2 grid_4.2.0
[121] rpart_4.1.16 rmarkdown_2.17 googledrive_2.0.0
[124] Rtsne_0.16 shiny_1.7.2 lubridate_1.8.0
[127] ggbeeswarm_0.6.0
This error also occurs if I extract the embeddings and metavars_df and run HarmonyMatrix.
I have traced the error to the following part of HarmonyMatrix.
phi <- Reduce(rbind, lapply(vars_use, function(var_use) {
t(onehot(meta_data[[var_use]]))
}))
Within this, it is the onehot function that is causing the error.
harmony:::onehot
function (x)
{
data.frame(x) %>% tibble::rowid_to_column("row_id") %>% dplyr::mutate(dummy = 1) %>%
tidyr::spread(x, .data$dummy, fill = 0) %>% dplyr::select(-.data$row_id) %>%
as.matrix
}
Changing dplyr::select(-.data$row_id) to dplyr::select(-row_id) fixes the issue.
Why it is working on my MacBook and not on CentOS 7 I can't explain since they are using the same version of dplyr.
I am also confused by the factor that the onehot function I find in harmony/utils.R looks completely different:
onehot <- function(x) {
res <- model.matrix(~0 + x)
colnames(res) <- gsub('^x(.*)', '\\1', colnames(res))
return(res)
}
I got the same error today. Using the following code before running RunHarmony solved my problem:
harmony.onehot.new <- function (x)
{
data.frame(x) %>% tibble::rowid_to_column("row_id") %>% dplyr::mutate(dummy = 1) %>%
tidyr::spread(x, .data$dummy, fill = 0) %>% dplyr::select(-row_id) %>%
as.matrix
}
environment(harmony.onehot.new) <- asNamespace('harmony')
assignInNamespace("onehot", harmony.onehot.new, ns = "harmony")
Reprex:
library(tidyverse)
onehot <- function (x) {
data.frame(x) %>%
tibble::rowid_to_column("row_id") %>%
dplyr::mutate(dummy = 1) %>%
tidyr::spread(x, .data$dummy, fill = 0) %>%
dplyr::select(-.data$row_id) %>%
as.matrix
}
donor <- factor(c("1", "2", "1", "3", "4", "2", "4", "1"))
onehot(donor)
#> Error in dplyr::select(., -.data$row_id): <text>:1:5: unexpected symbol
#> 1: Use of
#> ^
sessionInfo()
#> R version 4.2.0 (2022-04-22)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS: /Filers/package/R-base/4.2.0/lib64/R/lib/libRblas.so
#> LAPACK: /Filers/package/R-base/4.2.0/lib64/R/lib/libRlapack.so
#>
#> locale:
#> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
#> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
#> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10 purrr_0.3.5
#> [5] readr_2.1.3 tidyr_1.2.1 tibble_3.1.8 ggplot2_3.3.6
#> [9] tidyverse_1.3.2
#>
#> loaded via a namespace (and not attached):
#> [1] lubridate_1.8.0 assertthat_0.2.1 digest_0.6.29
#> [4] utf8_1.2.2 R6_2.5.1 cellranger_1.1.0
#> [7] backports_1.4.1 reprex_2.0.2 evaluate_0.17
#> [10] httr_1.4.4 highr_0.9 pillar_1.8.1
#> [13] rlang_1.0.5 googlesheets4_1.0.1 readxl_1.4.1
#> [16] rstudioapi_0.14 R.utils_2.12.0 R.oo_1.25.0
#> [19] rmarkdown_2.17 styler_1.7.0 googledrive_2.0.0
#> [22] munsell_0.5.0 broom_1.0.1 compiler_4.2.0
#> [25] modelr_0.1.9 xfun_0.30 pkgconfig_2.0.3
#> [28] htmltools_0.5.3 tidyselect_1.2.0 fansi_1.0.3
#> [31] crayon_1.5.2 tzdb_0.3.0 dbplyr_2.2.1
#> [34] withr_2.5.0 R.methodsS3_1.8.2 grid_4.2.0
#> [37] jsonlite_1.8.2 gtable_0.3.1 lifecycle_1.0.1
#> [40] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
#> [43] cli_3.4.1 stringi_1.7.8 fs_1.5.2
#> [46] xml2_1.3.3 ellipsis_0.3.2 generics_0.1.3
#> [49] vctrs_0.4.2 tools_4.2.0 R.cache_0.16.0
#> [52] glue_1.6.2 hms_1.1.2 fastmap_1.1.0
#> [55] yaml_2.3.5 colorspace_2.0-3 gargle_1.2.1
#> [58] rvest_1.0.3 knitr_1.40 haven_2.5.1