josschavezf
commented
3 weeks ago Hi @krigia what version of Giotto are you using? I tried running your code but I don't see any error. Maybe you can try with the most recent version (4.0.8) or even the development version (4.0.9) using remotes::install_github("drieslab/Giotto@suite_dev"). Here is my session info:
R version 4.4.0 (2024-04-24) Platform: x86_64-apple-darwin20 Running under: macOS Sonoma 14.5
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] Giotto_4.0.9 GiottoClass_0.3.2
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 viridisLite_0.4.2
[3] dplyr_1.1.4 GiottoVisuals_0.2.4
[5] fastmap_1.2.0 SingleCellExperiment_1.26.0
[7] lazyeval_0.2.2 digest_0.6.35
[9] lifecycle_1.0.4 terra_1.7-78
[11] magrittr_2.0.3 dbscan_1.1-12
[13] compiler_4.4.0 rlang_1.1.4
[15] tools_4.4.0 igraph_2.0.3
[17] utf8_1.2.4 data.table_1.15.4
[19] S4Arrays_1.4.1 htmlwidgets_1.6.4
[21] bit_4.0.5 sp_2.1-4
[23] reticulate_1.37.0 DelayedArray_0.30.1
[25] plyr_1.8.9 RColorBrewer_1.1-3
[27] abind_1.4-5 withr_3.0.0
[29] purrr_1.0.2 BiocGenerics_0.50.0
[31] grid_4.4.0 stats4_4.4.0
[33] fansi_1.0.6 colorspace_2.1-0
[35] ggplot2_3.5.1 scales_1.3.0
[37] gtools_3.9.5 SummarizedExperiment_1.34.0
[39] cli_3.6.2 crayon_1.5.2
[41] generics_0.1.3 rstudioapi_0.16.0
[43] httr_1.4.7 reshape2_1.4.4
[45] rjson_0.2.21 stringr_1.5.1
[47] zlibbioc_1.50.0 parallel_4.4.0
[49] XVector_0.44.0 matrixStats_1.3.0
[51] vctrs_0.6.5 Matrix_1.7-0
[53] jsonlite_1.8.8 IRanges_2.38.0
[55] S4Vectors_0.42.0 bit64_4.0.5
[57] ggrepel_0.9.5 scattermore_1.2
[59] hdf5r_1.3.10 magick_2.8.3
[61] GiottoUtils_0.1.9 plotly_4.10.4
[63] tidyr_1.3.1 glue_1.7.0
[65] codetools_0.2-20 cowplot_1.1.3
[67] stringi_1.8.4 gtable_0.3.5
[69] GenomeInfoDb_1.40.1 deldir_2.0-4
[71] GenomicRanges_1.56.0 UCSC.utils_1.0.0
[73] munsell_0.5.1 tibble_3.2.1
[75] pillar_1.9.0 htmltools_0.5.8.1
[77] GenomeInfoDbData_1.2.12 R6_2.5.1
[79] lattice_0.22-6 Biobase_2.64.0
[81] png_0.1-8 backports_1.5.0
[83] SpatialExperiment_1.14.0 Rcpp_1.0.12
[85] SparseArray_1.4.8 checkmate_2.3.1
[87] colorRamp2_0.1.0 MatrixGenerics_1.16.0
[89] pkgconfig_2.0.3
@gcyuan @bernard2012 @wwang-chcn @RubD I am getting the following error. The path are correct.
external python path provided and will be used
Error in createGiottoVisiumObject(h5_visium_path = data_path_F2_h5, h5_tissue_positions_path = data_path_F2_tissue_positions, : unused argument (h5_json_scalefactors_path = data_path_F2_scalefactors)
Thank you