Closed Jaimelan closed 3 months ago
Also, I attach the sessionInfo() output:
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Madrid
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] SeuratDisk_0.0.0.9021 Seurat_5.0.2 SeuratObject_5.0.1 sp_2.1-3 patchwork_1.2.0 CellChat_2.1.2 Biobase_2.62.0 BiocGenerics_0.48.1
[9] ggplot2_3.5.0 igraph_2.0.2 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.3.2 later_1.3.2 tibble_3.2.1 polyclip_1.10-6 ggnetwork_0.5.13 fastDummies_1.7.3 lifecycle_1.0.4
[9] rstatix_0.7.2 doParallel_1.0.17 globals_0.16.3 lattice_0.22-5 hdf5r_1.3.10 MASS_7.3-60.0.1 backports_1.4.1 magrittr_2.0.3
[17] plotly_4.10.4 sass_0.4.8 jquerylib_0.1.4 httpuv_1.6.14 NMF_0.27 sctransform_0.4.1 spam_2.10-0 spatstat.sparse_3.0-3
[25] reticulate_1.35.0 cowplot_1.1.3 pbapply_1.7-2 RColorBrewer_1.1-3 abind_1.4-5 Rtsne_0.17 purrr_1.0.2 presto_1.0.0
[33] circlize_0.4.16 IRanges_2.36.0 S4Vectors_0.40.2 ggrepel_0.9.5 irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.0-4 goftest_1.2-3
[41] RSpectra_0.16-1 spatstat.random_3.2-3 fitdistrplus_1.1-11 parallelly_1.37.1 svglite_2.1.3 leiden_0.4.3.1 codetools_0.2-19 tidyselect_1.2.0
[49] shape_1.4.6.1 matrixStats_1.2.0 stats4_4.3.2 spatstat.explore_3.2-6 jsonlite_1.8.8 GetoptLong_1.0.5 BiocNeighbors_1.20.2 ellipsis_0.3.2
[57] progressr_0.14.0 ggridges_0.5.6 ggalluvial_0.12.5 survival_3.5-7 iterators_1.0.14 systemfonts_1.0.6 foreach_1.5.2 tools_4.3.2
[65] sna_2.7-2 ica_1.0-3 Rcpp_1.0.12 glue_1.7.0 gridExtra_2.3 withr_3.0.0 BiocManager_1.30.22 fastmap_1.1.1
[73] fansi_1.0.6 digest_0.6.34 R6_2.5.1 mime_0.12 colorspace_2.1-0 scattermore_1.2 tensor_1.5 spatstat.data_3.0-4
[81] utf8_1.2.4 tidyr_1.3.1 generics_0.1.3 renv_1.0.5 data.table_1.15.2 FNN_1.1.4 httr_1.4.7 htmlwidgets_1.6.4
[89] uwot_0.1.16 pkgconfig_2.0.3 gtable_0.3.4 registry_0.5-1 ComplexHeatmap_2.18.0 lmtest_0.9-40 htmltools_0.5.7 carData_3.0-5
[97] dotCall64_1.1-1 clue_0.3-65 scales_1.3.0 tidyverse_2.0.0 png_0.1-8 rstudioapi_0.15.0 reshape2_1.4.4 rjson_0.2.21
[105] coda_0.19-4.1 statnet.common_4.9.0 nlme_3.1-163 cachem_1.0.8 zoo_1.8-12 GlobalOptions_0.1.2 stringr_1.5.1 KernSmooth_2.23-22
[113] parallel_4.3.2 miniUI_0.1.1.1 pillar_1.9.0 grid_4.3.2 vctrs_0.6.5 RANN_2.6.1 promises_1.2.1 ggpubr_0.6.0
[121] car_3.1-2 xtable_1.8-4 cluster_2.1.6 cli_3.6.2 compiler_4.3.2 rlang_1.1.3 crayon_1.5.2 rngtools_1.5.2
[129] future.apply_1.11.1 ggsignif_0.6.4 plyr_1.8.9 stringi_1.8.3 viridisLite_0.4.2 network_1.18.2 deldir_2.0-4 gridBase_0.4-7
[137] BiocParallel_1.36.0 munsell_0.5.0 lazyeval_0.2.2 spatstat.geom_3.2-9 Matrix_1.6-5 RcppHNSW_0.6.0 bit64_4.0.5 future_1.33.1
[145] shiny_1.8.0 ROCR_1.0-11 broom_1.0.5 bslib_0.6.1 bit_4.0.5
```R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Madrid
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] SeuratDisk_0.0.0.9021 Seurat_5.0.2 SeuratObject_5.0.1 sp_2.1-3 patchwork_1.2.0 CellChat_2.1.2 Biobase_2.62.0 BiocGenerics_0.48.1
[9] ggplot2_3.5.0 igraph_2.0.2 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.3.2 later_1.3.2 tibble_3.2.1 polyclip_1.10-6 ggnetwork_0.5.13 fastDummies_1.7.3 lifecycle_1.0.4
[9] rstatix_0.7.2 doParallel_1.0.17 globals_0.16.3 lattice_0.22-5 hdf5r_1.3.10 MASS_7.3-60.0.1 backports_1.4.1 magrittr_2.0.3
[17] plotly_4.10.4 sass_0.4.8 jquerylib_0.1.4 httpuv_1.6.14 NMF_0.27 sctransform_0.4.1 spam_2.10-0 spatstat.sparse_3.0-3
[25] reticulate_1.35.0 cowplot_1.1.3 pbapply_1.7-2 RColorBrewer_1.1-3 abind_1.4-5 Rtsne_0.17 purrr_1.0.2 presto_1.0.0
[33] circlize_0.4.16 IRanges_2.36.0 S4Vectors_0.40.2 ggrepel_0.9.5 irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.0-4 goftest_1.2-3
[41] RSpectra_0.16-1 spatstat.random_3.2-3 fitdistrplus_1.1-11 parallelly_1.37.1 svglite_2.1.3 leiden_0.4.3.1 codetools_0.2-19 tidyselect_1.2.0
[49] shape_1.4.6.1 matrixStats_1.2.0 stats4_4.3.2 spatstat.explore_3.2-6 jsonlite_1.8.8 GetoptLong_1.0.5 BiocNeighbors_1.20.2 ellipsis_0.3.2
[57] progressr_0.14.0 ggridges_0.5.6 ggalluvial_0.12.5 survival_3.5-7 iterators_1.0.14 systemfonts_1.0.6 foreach_1.5.2 tools_4.3.2
[65] sna_2.7-2 ica_1.0-3 Rcpp_1.0.12 glue_1.7.0 gridExtra_2.3 withr_3.0.0 BiocManager_1.30.22 fastmap_1.1.1
[73] fansi_1.0.6 digest_0.6.34 R6_2.5.1 mime_0.12 colorspace_2.1-0 scattermore_1.2 tensor_1.5 spatstat.data_3.0-4
[81] utf8_1.2.4 tidyr_1.3.1 generics_0.1.3 renv_1.0.5 data.table_1.15.2 FNN_1.1.4 httr_1.4.7 htmlwidgets_1.6.4
[89] uwot_0.1.16 pkgconfig_2.0.3 gtable_0.3.4 registry_0.5-1 ComplexHeatmap_2.18.0 lmtest_0.9-40 htmltools_0.5.7 carData_3.0-5
[97] dotCall64_1.1-1 clue_0.3-65 scales_1.3.0 tidyverse_2.0.0 png_0.1-8 rstudioapi_0.15.0 reshape2_1.4.4 rjson_0.2.21
[105] coda_0.19-4.1 statnet.common_4.9.0 nlme_3.1-163 cachem_1.0.8 zoo_1.8-12 GlobalOptions_0.1.2 stringr_1.5.1 KernSmooth_2.23-22
[113] parallel_4.3.2 miniUI_0.1.1.1 pillar_1.9.0 grid_4.3.2 vctrs_0.6.5 RANN_2.6.1 promises_1.2.1 ggpubr_0.6.0
[121] car_3.1-2 xtable_1.8-4 cluster_2.1.6 cli_3.6.2 compiler_4.3.2 rlang_1.1.3 crayon_1.5.2 rngtools_1.5.2
[129] future.apply_1.11.1 ggsignif_0.6.4 plyr_1.8.9 stringi_1.8.3 viridisLite_0.4.2 network_1.18.2 deldir_2.0-4 gridBase_0.4-7
[137] BiocParallel_1.36.0 munsell_0.5.0 lazyeval_0.2.2 spatstat.geom_3.2-9 Matrix_1.6-5 RcppHNSW_0.6.0 bit64_4.0.5 future_1.33.1
[145] shiny_1.8.0 ROCR_1.0-11 broom_1.0.5 bslib_0.6.1 bit_4.0.5
@Jaimelan I feel this issue may be related to the input cell group information. The cell names in cell group labels are not the same with the cell names in the spatial coordinates. You can check this in the cellchat object. Otherwise, you have to run the source codes one by one to figure out the reason.
I checked them to be concordant and it worked just fine. Thanks for the tip and you work with this software!
So I have been receiving the following error when trying to plot a
cellchat
object computed from aSeurat
object from spatial transcriptomics data (Visium 10x):Error in names(x) <- value : 'names' attribute [4] must be the same length as the vector [2]
I am working with Cellchat v2.1.2 and Seurat v5.0.2 and the traceback of the error is:
Where the function in 1 receives a cellchat object and the name of the pathway to plot in the spatial plot of communications.
I am not sure what is failing in the process, the objects were created following the available tutorial for spatial published in this repo, and I am struggling to identify the origin of the 4 attributes expected by the function in
`colnames<-
(*tmp*
, value = c("X1", "Y1", "X2", "Y2")) at visualization.R#1554`Thank you for your work developing this package and for your attention.
Best, Jaime