Transformation between Seurat and Giotto object

[howtofindme]

dear RubD,

Thank you for your excellent job! I Have a visium Seurat object. How can I Transform it to Giotto visum object in a quickly way ?

hoping to hear from you ,
best wishes

[szheng29]

Hi,

We have a function called seuratToGiotto() in the suite branch, which enables transforming a Seurat object to Giotto.

[joe-jhou2]

Hi when I use seuratToGiotto() for seurat object, it returns an error "in seuratToGiotto(se.subset) : object 'test' not found". No clue what it is. Can you provide some insights? Thanks

[EmmaKelley]

Hi,

Which version of suite are you using? You may have to update if you are not using the current version, 2.0.0.998.

If that does not work could you provide the a screen shot with what happens when you run seuratToGiotto?

[joe-jhou2]

It's the latest version

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] harmony_0.1.0 Rcpp_1.0.8.3 STutility_0.1.0 ggplot2_3.3.6 SeuratObject_4.0.4 Seurat_4.1.0 NNLM_0.4.4
[8] Giotto_2.0.0.998

loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.24 tidyselect_1.1.2 htmlwidgets_1.5.4 BiocParallel_1.24.1 grid_4.0.3
[7] Rtsne_0.16 munsell_0.5.0 codetools_0.2-18 ica_1.0-2 units_0.8-0 future_1.25.0
[13] miniUI_0.1.1.1 withr_2.5.0 spatstat.random_2.2-0 colorspace_2.0-3 knitr_1.39 uuid_1.1-0
[19] stats4_4.0.3 ROCR_1.0-11 wk_0.6.0 tensor_1.5 Rttf2pt1_1.3.10 listenv_0.8.0
[25] MatrixGenerics_1.2.1 labeling_0.4.2 polyclip_1.10-0 bit64_4.0.5 farver_2.1.0 pheatmap_1.0.12
[31] rprojroot_2.0.3 parallelly_1.31.1 vctrs_0.4.1 generics_0.1.2 xfun_0.30 R6_2.5.1
[37] doParallel_1.0.17 rsvd_1.0.5 Morpho_2.9 hdf5r_1.3.5 ggiraph_0.8.2 RcppZiggurat_0.1.6
[43] DelayedArray_0.16.3 spatstat.utils_2.3-0 assertthat_0.2.1 promises_1.2.0.1 scales_1.2.0 imager_0.42.13
[49] gtable_0.3.0 beachmat_2.6.4 globals_0.15.0 bmp_0.3 goftest_1.2-3 rlang_1.0.2
[55] zeallot_0.1.0 akima_0.6-3.4 systemfonts_1.0.4 splines_4.0.3 extrafontdb_1.0 lazyeval_0.2.2
[61] spatstat.geom_2.4-0 s2_1.0.7 rgl_0.108.3 reshape2_1.4.4 abind_1.4-5 Rfast_2.0.6
[67] httpuv_1.6.5 extrafont_0.18 tools_4.0.3 spData_2.0.1 ellipsis_0.3.2 spatstat.core_2.4-2
[73] raster_3.5-15 RColorBrewer_1.1-3 BiocGenerics_0.36.1 proxy_0.4-26 Rvcg_0.21 ggridges_0.5.3
[79] plyr_1.8.7 classInt_0.4-3 purrr_0.3.4 rpart_4.1.16 dbscan_1.1-10 deldir_1.0-6
[85] pbapply_1.5-0 viridis_0.6.2 cowplot_1.1.1 S4Vectors_0.28.1 zoo_1.8-10 ggrepel_0.9.1
[91] cluster_2.1.3 colorRamps_2.3.1 here_1.0.1 tinytex_0.38 magrittr_2.0.3 RSpectra_0.16-1
[97] data.table_1.14.2 magick_2.7.3 scattermore_0.8 readbitmap_0.1.5 lmtest_0.9-40 RANN_2.6.1
[103] fitdistrplus_1.1-8 matrixStats_0.62.0 patchwork_1.1.1 shinyjs_2.1.0 mime_0.12 xtable_1.8-4
[109] jpeg_0.1-9 IRanges_2.24.1 gridExtra_2.3 compiler_4.0.3 tibble_3.1.7 KernSmooth_2.23-20
[115] crayon_1.5.1 htmltools_0.5.2 mgcv_1.8-40 later_1.3.0 spdep_1.2-4 tiff_0.1-11
[121] tidyr_1.2.0 DBI_1.1.2 MASS_7.3-57 sf_1.0-7 boot_1.3-28 Matrix_1.4-1
[127] cli_3.3.0 quadprog_1.5-8 parallel_4.0.3 igraph_1.3.1 pkgconfig_2.0.3 sp_1.4-7
[133] terra_1.5-21 plotly_4.10.0 spatstat.sparse_2.1-1 foreach_1.5.2 stringr_1.4.0 bezier_1.1.2
[139] digest_0.6.29 sctransform_0.3.3 RcppAnnoy_0.0.19 spatstat.data_2.2-0 leiden_0.3.10 uwot_0.1.11
[145] shiny_1.7.1 lifecycle_1.0.1 nlme_3.1-157 jsonlite_1.8.0 viridisLite_0.4.0 fansi_1.0.3
[151] pillar_1.7.0 lattice_0.20-45 fastmap_1.1.0 httr_1.4.3 survival_3.3-1 glue_1.6.2
[157] remotes_2.4.2 FNN_1.1.3 png_0.1-7 iterators_1.0.14 bit_4.0.4 class_7.3-20
[163] stringi_1.7.6 BiocSingular_1.6.0 dplyr_1.0.9 irlba_2.3.5 e1071_1.7-9 future.apply_1.9.0

[joe-jhou2]

That error is gone when reboot the R. But another error shows " Error: Cannot find 'pca' in this Seurat object".
I retrieve your code, yes, only "pca" data extract for Dimension Reduction slot. My data was processed by harmony and NMF instead of PCA. Even I revise your code to accommodate my case, but the downstream analysis cannot pass through.
Simplify my question, I'd like to try your spatial deconvolution algorithm on my Seurat object which has been processed by harmony and NMF only. Any suggestion to implement that ? Thanks.

[EternalEnvy10]

sessionInfo()

Hi,

Which version of suite are you using? You may have to update if you are not using the current version, 2.0.0.998.

If that does not work could you provide the a screen shot with what happens when you run seuratToGiotto?

How do I upgrade packages? I find that using update.packages() does not work.

[EmmaKelley]

Suite is our development branch and has not been officially released, as such is frequently updated. In order to make sure you are using the most up-to-date version, it is best practice to re-install Giotto suite regularly:

remotes::install_github("RubD/Giotto@suite")

[EmmaKelley]

The SeurattoGiotto issue that opened this thread should be fixed now as the function is now compatible with Seurat objects with any type of dimension reduction.

[EternalEnvy10]

Suite is our development branch and has not been officially released, as such is frequently updated. In order to make sure you are using the most up-to-date version, it is best practice to re-install Giotto suite regularly:

remotes::install_github("RubD/Giotto@suite")

Thank you for your reply!
I have now converted the Seurat object into a Giotto object. I want to perform a spatial patterns analysis based on the clusters that Seurat has divided. I refer to the mouse_visium_brain demo.
So I run the process from part8:spatial grid：

The error message is as follows：

Did I miss an important process that led to an error?
Looking forward to your reply:)

Best,
Zhaonian