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Published
20 hours ago •
satijalab
satijalab
Crop with SpatialPlot with Seurat 4.1 dev branch
Hi,
Like previous issues #4411, #2700 , I am facing some issue with the crop option with my data :
Crop=False
Crop=True
As most of advice were to use dev branch, I did it but it did not resolve my issue (results from dev branch are above).
install.packages('remotes')
remotes::install_github(repo = 'satijalab/seurat', ref = 'develop')
library(Seurat)
Installing package into ‘/home/eugene/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/remotes_2.4.2.tar.gz'
Content type 'application/x-gzip' length 152540 bytes (148 KB)
==================================================
downloaded 148 KB
* installing *source* package ‘remotes’ ...
** package ‘remotes’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (remotes)
The downloaded source packages are in
‘/tmp/Rtmp2AqIhA/downloaded_packages’
Skipping install of 'Seurat' from a github remote, the SHA1 (eaaf6750) has not changed since last install.
Use `force = TRUE` to force installation
SessionInfo:
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 21.10
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.7 patchwork_1.1.1 ggplot2_3.3.5
[4] SeuratDisk_0.0.0.9019 SeuratData_0.2.1 SeuratObject_4.0.4
[7] Seurat_4.1.0
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_2.0-2 deldir_1.0-6
[4] ellipsis_0.3.2 ggridges_0.5.3 rprojroot_2.0.2
[7] spatstat.data_2.1-2 farver_2.1.0 leiden_0.3.9
[10] listenv_0.8.0 remotes_2.4.2 ggrepel_0.9.1
[13] bit64_4.0.5 fansi_1.0.2 codetools_0.2-18
[16] splines_4.1.2 polyclip_1.10-0 jsonlite_1.7.3
[19] ica_1.0-2 cluster_2.1.2 png_0.1-7
[22] uwot_0.1.11 shiny_1.7.1 sctransform_0.3.3
[25] spatstat.sparse_2.1-0 compiler_4.1.2 httr_1.4.2
[28] assertthat_0.2.1 Matrix_1.3-4 fastmap_1.1.0
[31] lazyeval_0.2.2 cli_3.1.1 later_1.3.0
[34] htmltools_0.5.2 prettyunits_1.1.1 tools_4.1.2
[37] igraph_1.2.11 gtable_0.3.0 glue_1.6.1
[40] RANN_2.6.1 reshape2_1.4.4 rappdirs_0.3.3
[43] Rcpp_1.0.8 scattermore_0.7 vctrs_0.3.8
[46] nlme_3.1-155 lmtest_0.9-39 stringr_1.4.0
[49] globals_0.14.0 ps_1.6.0 mime_0.12
[52] miniUI_0.1.1.1 lifecycle_1.0.1 irlba_2.3.5
[55] goftest_1.2-3 future_1.23.0 MASS_7.3-54
[58] zoo_1.8-9 scales_1.1.1 spatstat.core_2.3-2
[61] promises_1.2.0.1 spatstat.utils_2.3-0 parallel_4.1.2
[64] RColorBrewer_1.1-2 curl_4.3.2 reticulate_1.23
[67] pbapply_1.5-0 gridExtra_2.3 rpart_4.1-15
[70] stringi_1.7.6 pkgbuild_1.3.1 rlang_0.4.12
[73] pkgconfig_2.0.3 matrixStats_0.61.0 lattice_0.20-45
[76] ROCR_1.0-11 purrr_0.3.4 tensor_1.5
[79] labeling_0.4.2 htmlwidgets_1.5.4 bit_4.0.4
[82] cowplot_1.1.1 tidyselect_1.1.1 processx_3.5.2
[85] parallelly_1.30.0 RcppAnnoy_0.0.19 plyr_1.8.6
[88] magrittr_2.0.1 R6_2.5.1 generics_0.1.1
[91] DBI_1.1.2 pillar_1.6.4 withr_2.4.3
[94] mgcv_1.8-38 fitdistrplus_1.1-6 survival_3.2-13
[97] abind_1.4-5 tibble_3.1.6 future.apply_1.8.1
[100] crayon_1.4.2 hdf5r_1.3.5 KernSmooth_2.23-20
[103] utf8_1.2.2 spatstat.geom_2.3-1 plotly_4.10.0
[106] grid_4.1.2 data.table_1.14.2 callr_3.7.0
[109] digest_0.6.29 xtable_1.8-4 tidyr_1.1.4
[112] httpuv_1.6.5 munsell_0.5.0 viridisLite_0.4.0
I can not share the data publicly on github, but I can share an .rds by email if required to fix the issue.
Best, WesDe
Hi @WesDe ,
Can you try updating the ggplot2 to the latest version, reinstalling Seurat and check the data again ?
Hi @k3yavi,
I have updated ggplot2 and Seurat but the issue remains.
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 21.10
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SeuratObject_4.0.4 Seurat_4.1.0 ggplot2_3.3.5
loaded via a namespace (and not attached):
[1] nlme_3.1-155 matrixStats_0.61.0 spatstat.sparse_2.1-0
[4] bit64_4.0.5 RcppAnnoy_0.0.19 RColorBrewer_1.1-2
[7] httr_1.4.2 sctransform_0.3.3 tools_4.1.2
[10] utf8_1.2.2 R6_2.5.1 irlba_2.3.5
[13] rpart_4.1.16 KernSmooth_2.23-20 uwot_0.1.11
[16] mgcv_1.8-38 DBI_1.1.2 lazyeval_0.2.2
[19] colorspace_2.0-2 withr_2.4.3 tidyselect_1.1.1
[22] gridExtra_2.3 bit_4.0.4 compiler_4.1.2
[25] cli_3.1.1 hdf5r_1.3.5 plotly_4.10.0
[28] labeling_0.4.2 scales_1.1.1 lmtest_0.9-39
[31] spatstat.data_2.1-2 ggridges_0.5.3 pbapply_1.5-0
[34] goftest_1.2-3 stringr_1.4.0 digest_0.6.29
[37] spatstat.utils_2.3-0 pkgconfig_2.0.3 htmltools_0.5.2
[40] parallelly_1.30.0 fastmap_1.1.0 htmlwidgets_1.5.4
[43] rlang_1.0.0 shiny_1.7.1 farver_2.1.0
[46] generics_0.1.1 zoo_1.8-9 jsonlite_1.7.3
[49] ica_1.0-2 dplyr_1.0.7 magrittr_2.0.2
[52] patchwork_1.1.1 Matrix_1.4-0 Rcpp_1.0.8
[55] munsell_0.5.0 fansi_1.0.2 abind_1.4-5
[58] reticulate_1.24 lifecycle_1.0.1 stringi_1.7.6
[61] MASS_7.3-55 Rtsne_0.15 plyr_1.8.6
[64] grid_4.1.2 parallel_4.1.2 listenv_0.8.0
[67] promises_1.2.0.1 ggrepel_0.9.1 crayon_1.4.2
[70] deldir_1.0-6 miniUI_0.1.1.1 lattice_0.20-45
[73] cowplot_1.1.1 splines_4.1.2 tensor_1.5
[76] pillar_1.6.5 igraph_1.2.11 spatstat.geom_2.3-1
[79] future.apply_1.8.1 reshape2_1.4.4 codetools_0.2-18
[82] leiden_0.3.9 glue_1.6.1 data.table_1.14.2
[85] png_0.1-7 vctrs_0.3.8 httpuv_1.6.5
[88] polyclip_1.10-0 gtable_0.3.0 RANN_2.6.1
[91] purrr_0.3.4 spatstat.core_2.3-2 tidyr_1.1.4
[94] scattermore_0.7 future_1.23.0 assertthat_0.2.1
[97] mime_0.12 xtable_1.8-4 later_1.3.0
[100] survival_3.2-13 viridisLite_0.4.0 tibble_3.1.6
[103] cluster_2.1.2 globals_0.14.0 fitdistrplus_1.1-6
[106] ellipsis_0.3.2 ROCR_1.0-11
With the latest version of Seurat 4.1.1 and ggplot2 3.3.6, the issue still remains!
Hi, This bug does not seem to exist for the latest version of Seurat. I am closing this issue now but feel free to re-open it if the issue persists.
Hi,
I have the same issue. I have installed the last versions of seurat and ggplot2.
Here is an example of the spatialdimplot I can obtain.
I have tested your sagittal Brain dataset ( from the fastq) and the plot were as expected.
Can you help me please?
Thanks a lot!
Christelle
