Open cvw462 opened 1 year ago
Hi,
I want to create a spatial dim plot after subsetting data based on expression of a rare gene.
Library(Seurat) Library(ggplot2) Library(patchwork) Library(dplyr)
spleen <- subset(controlspleen.rds, subset = gene > 0) spatialdimplot(spleen)
IT RETURNS THIS ERROR*
Error in grid.Call.graphics(C_raster, x$raster, x$x, x$y, x$width, x$height, : cannot allocate memory block of size 67108864 Tb
R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /apps/R/4.1.1/lib64/R/lib/libRblas.so LAPACK: /apps/R/4.1.1/lib64/R/lib/libRlapack.so locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets [6] methods base other attached packages: [1] dplyr_1.0.8 patchwork_1.1.1 ggplot2_3.3.5 [4] SeuratObject_4.0.4 Seurat_4.1.0 loaded via a namespace (and not attached): [1] nlme_3.1-152 matrixStats_0.62.0 [3] spatstat.sparse_2.1-1 RcppAnnoy_0.0.19 [5] RColorBrewer_1.1-3 httr_1.4.2 [7] sctransform_0.3.3 tools_4.1.1 [9] utf8_1.2.2 R6_2.5.1 [11] irlba_2.3.5 rpart_4.1-15 [13] KernSmooth_2.23-20 uwot_0.1.11 [15] mgcv_1.8-36 DBI_1.1.2 [17] lazyeval_0.2.2 colorspace_2.0-3 [19] withr_2.5.0 tidyselect_1.1.2 [21] gridExtra_2.3 compiler_4.1.1 [23] cli_3.3.0 plotly_4.10.0 [25] labeling_0.4.2 scales_1.2.0 [27] lmtest_0.9-40 spatstat.data_2.2-0 [29] ggridges_0.5.3 pbapply_1.5-0 [31] goftest_1.2-3 stringr_1.4.0 [33] digest_0.6.29 spatstat.utils_2.3-0 [35] pkgconfig_2.0.3 htmltools_0.5.2 [37] parallelly_1.31.1 fastmap_1.1.0 [39] htmlwidgets_1.5.4 rlang_1.0.2 [41] rstudioapi_0.13 shiny_1.7.1 [43] farver_2.1.0 generics_0.1.2 [45] zoo_1.8-10 jsonlite_1.8.0 [47] ica_1.0-2 spatst
Hi,
I want to create a spatial dim plot after subsetting data based on expression of a rare gene.
Library(Seurat) Library(ggplot2) Library(patchwork) Library(dplyr)
spleen <- subset(controlspleen.rds, subset = gene > 0) spatialdimplot(spleen)
IT RETURNS THIS ERROR*
Error in grid.Call.graphics(C_raster, x$raster, x$x, x$y, x$width, x$height, : cannot allocate memory block of size 67108864 Tb
R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /apps/R/4.1.1/lib64/R/lib/libRblas.so LAPACK: /apps/R/4.1.1/lib64/R/lib/libRlapack.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 [6] methods base other attached packages: [1] dplyr_1.0.8 patchwork_1.1.1 ggplot2_3.3.5 [4] SeuratObject_4.0.4 Seurat_4.1.0 loaded via a namespace (and not attached): [1] nlme_3.1-152 matrixStats_0.62.0 [3] spatstat.sparse_2.1-1 RcppAnnoy_0.0.19 [5] RColorBrewer_1.1-3 httr_1.4.2 [7] sctransform_0.3.3 tools_4.1.1 [9] utf8_1.2.2 R6_2.5.1 [11] irlba_2.3.5 rpart_4.1-15 [13] KernSmooth_2.23-20 uwot_0.1.11 [15] mgcv_1.8-36 DBI_1.1.2 [17] lazyeval_0.2.2 colorspace_2.0-3 [19] withr_2.5.0 tidyselect_1.1.2 [21] gridExtra_2.3 compiler_4.1.1 [23] cli_3.3.0 plotly_4.10.0 [25] labeling_0.4.2 scales_1.2.0 [27] lmtest_0.9-40 spatstat.data_2.2-0 [29] ggridges_0.5.3 pbapply_1.5-0 [31] goftest_1.2-3 stringr_1.4.0 [33] digest_0.6.29 spatstat.utils_2.3-0 [35] pkgconfig_2.0.3 htmltools_0.5.2 [37] parallelly_1.31.1 fastmap_1.1.0 [39] htmlwidgets_1.5.4 rlang_1.0.2 [41] rstudioapi_0.13 shiny_1.7.1 [43] farver_2.1.0 generics_0.1.2 [45] zoo_1.8-10 jsonlite_1.8.0 [47] ica_1.0-2 spatst