hto_dist_mtx <- as.matrix(dist(t(GetAssayData(seurat_obj, assay = "HTO"))))
seurat_obj <- RunTSNE(seurat_obj, distance.matrix = hto_dist_mtx,
perplexity = 100, reduction.name = "tsnedist")
I am getting the error below. What does this mean and is there a way for me to fix this? Does it relate to the size of the matrix? I have 60,000 cells and six hashtag antibodies.
9. complete.cases(object)
8. na.fail.default(X)
7. na.fail(X)
6. Rtsne.default(X = object, dims = dim.embed, pca = FALSE, ...)
5. Rtsne(X = object, dims = dim.embed, pca = FALSE, ...)
4. RunTSNE.matrix(object = distance.matrix, assay = DefaultAssay(object = object),
seed.use = seed.use, tsne.method = tsne.method, dim.embed = dim.embed,
reduction.key = reduction.key, is_distance = TRUE, ...)
3. RunTSNE(object = distance.matrix, assay = DefaultAssay(object = object),
seed.use = seed.use, tsne.method = tsne.method, dim.embed = dim.embed,
reduction.key = reduction.key, is_distance = TRUE, ...)
2. RunTSNE.Seurat(seurat_obj, distance.matrix = hto_dist_mtx, perplexity = 100,
reduction.name = "tsnedist")
1. RunTSNE(seurat_obj, distance.matrix = hto_dist_mtx, perplexity = 100,
reduction.name = "tsnedist")
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] cellhashR_1.0.3 forcats_0.5.2 stringr_1.4.1
[4] dplyr_1.0.10 purrr_0.3.5 readr_2.1.3
[7] tidyr_1.2.1 tibble_3.1.8 ggplot2_3.3.6
[10] tidyverse_1.3.2 sp_1.5-0 SeuratObject_4.1.2.9003
[13] Seurat_4.2.0.9001
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_0.6.30
[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 vroom_1.6.0
[22] spatstat.sparse_3.0-0 rmdformats_1.0.4 colorspace_2.0-3
[25] rvest_1.0.3 ggrepel_0.9.1 haven_2.5.1
[28] xfun_0.34 crayon_1.5.2 jsonlite_1.8.3
[31] progressr_0.11.0 spatstat.data_3.0-0 survival_3.4-0
[34] zoo_1.8-11 glue_1.6.2 polyclip_1.10-4
[37] gtable_0.3.1 gargle_1.2.1 leiden_0.4.3
[40] future.apply_1.9.1 abind_1.4-5 scales_1.2.1
[43] DBI_1.1.3 spatstat.random_2.2-0 miniUI_0.1.1.1
[46] Rcpp_1.0.9 viridisLite_0.4.1 xtable_1.8-4
[49] reticulate_1.26 spatstat.core_2.4-4 bit_4.0.4
[52] htmlwidgets_1.5.4 httr_1.4.4 RColorBrewer_1.1-3
[55] ellipsis_0.3.2 ica_1.0-3 farver_2.1.1
[58] pkgconfig_2.0.3 uwot_0.1.14 dbplyr_2.2.1
[61] deldir_1.0-6 utf8_1.2.2 labeling_0.4.2
[64] tidyselect_1.2.0 rlang_1.0.6 reshape2_1.4.4
[67] later_1.3.0 munsell_0.5.0 cellranger_1.1.0
[70] tools_4.2.0 cli_3.4.1 generics_0.1.3
[73] broom_1.0.1 ggridges_0.5.4 evaluate_0.17
[76] fastmap_1.1.0 yaml_2.3.6 goftest_1.2-3
[79] bit64_4.0.5 knitr_1.40 fs_1.5.2
[82] fitdistrplus_1.1-8 RANN_2.6.1 pbapply_1.5-0
[85] future_1.28.0 nlme_3.1-160 mime_0.12
[88] ggrastr_1.0.1 xml2_1.3.3 compiler_4.2.0
[91] rstudioapi_0.14 beeswarm_0.4.0 plotly_4.10.0
[94] png_0.1-7 spatstat.utils_3.0-1 reprex_2.0.2
[97] stringi_1.7.8 rgeos_0.5-9 lattice_0.20-45
[100] Matrix_1.5-1 vctrs_0.5.0 pillar_1.8.1
[103] lifecycle_1.0.3 spatstat.geom_3.0-3 lmtest_0.9-40
[106] RcppAnnoy_0.0.20 data.table_1.14.4 cowplot_1.1.1
[109] irlba_2.3.5.1 httpuv_1.6.6 patchwork_1.1.2
[112] R6_2.5.1 bookdown_0.29 promises_1.2.0.1
[115] KernSmooth_2.23-20 gridExtra_2.3 vipor_0.4.5
[118] parallelly_1.32.1 codetools_0.2-18 MASS_7.3-58.1
[121] assertthat_0.2.1 withr_2.5.0 sctransform_0.3.5
[124] mgcv_1.8-41 parallel_4.2.0 hms_1.1.2
[127] grid_4.2.0 rpart_4.1.19 rmarkdown_2.17
[130] googledrive_2.0.0 Rtsne_0.16 shiny_1.7.3
[133] lubridate_1.8.0 ggbeeswarm_0.6.0