projectData has been removed from NAMESPACE but is still in tutorials
Opened this issue · 9 comments
According to the tutorials, projectData() can be called to smooth expression values, however, this function is no longer exported.
Should smoothData() be used instead?
Thanks
Hilmar
@sqjin Is this change not going to be documented in the vignettes? Also, when replacing the function with smoothData a new error is presented: cellchat <- smoothData(cellchat, PPI.mouse)
Error in smoothData(cellchat, PPI.mouse) : object 'adjMatrix' not found
I also encountered the same problem. The latest version of the "projectData" function is not available. The "smoothData" function is reporting an error...
@monikaramos @ibzhuai This error has been fixed. Please re-install it. We will update the vignettes later.
@sqjin The error is not fixed. I re-installed cellchat and restarted my R as well.
@sqjin I also checked PPI.mouse and it is indeed a sparseMatrix:
@monikaramos It should be run as follows.
cellchat <- smoothData(cellchat, adj = PPI.human)
Hello, I am having similar problems. I was able to swap the command for projectData to smoothData, but I am now getting the following error:
cellchat_obj <- smoothData(cellchat_obj, adj = PPI.mouse)
Error in solve.default(AA, BB) : no right-hand side in 'b'
I just installed cellchat today (6/21/24). Here is my R Session info:
sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 9.3 (Blue Onyx)
Matrix products: default
BLAS: /opt/R-4.4.1/lib64/R/lib/libRblas.so
LAPACK: /opt/R-4.4.1/lib64/R/lib/libRlapack.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: US/Eastern
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] CellChat_2.1.2 Biobase_2.64.0 BiocGenerics_0.50.0 ggplot2_3.5.1 igraph_2.0.3 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.4.1 later_1.3.2 tibble_3.2.1 polyclip_1.10-6 ggnetwork_0.5.13
[7] fastDummies_1.7.3 lifecycle_1.0.4 rstatix_0.7.2 doParallel_1.0.17 globals_0.16.3 lattice_0.22-6
[13] MASS_7.3-60.2 backports_1.5.0 magrittr_2.0.3 plotly_4.10.4 sass_0.4.9 jquerylib_0.1.4
[19] remotes_2.5.0 httpuv_1.6.15 Seurat_5.1.0 NMF_0.27 sctransform_0.4.1 spam_2.10-0
[25] sp_2.1-4 sessioninfo_1.2.2 pkgbuild_1.4.4 spatstat.sparse_3.1-0 reticulate_1.38.0 cowplot_1.1.3
[31] pbapply_1.7-2 RColorBrewer_1.1-3 abind_1.4-5 pkgload_1.3.4 Rtsne_0.17 purrr_1.0.2
[37] circlize_0.4.16 IRanges_2.38.0 S4Vectors_0.42.0 ggrepel_0.9.5 irlba_2.3.5.1 listenv_0.9.1
[43] spatstat.utils_3.0-5 goftest_1.2-3 RSpectra_0.16-1 spatstat.random_3.2-3 fitdistrplus_1.1-11 parallelly_1.37.1
[49] svglite_2.1.3 leiden_0.4.3.1 codetools_0.2-20 tidyselect_1.2.1 shape_1.4.6.1 matrixStats_1.3.0
[55] stats4_4.4.1 spatstat.explore_3.2-7 jsonlite_1.8.8 GetoptLong_1.0.5 BiocNeighbors_1.22.0 ellipsis_0.3.2
[61] progressr_0.14.0 ggridges_0.5.6 ggalluvial_0.12.5 survival_3.6-4 iterators_1.0.14 systemfonts_1.1.0
[67] foreach_1.5.2 tools_4.4.1 sna_2.7-2 ica_1.0-3 Rcpp_1.0.12 glue_1.7.0
[73] gridExtra_2.3 usethis_2.2.3 withr_3.0.0 BiocManager_1.30.23 fastmap_1.2.0 fansi_1.0.6
[79] digest_0.6.35 R6_2.5.1 mime_0.12 colorspace_2.1-0 scattermore_1.2 tensor_1.5
[85] spatstat.data_3.1-2 utf8_1.2.4 tidyr_1.3.1 generics_0.1.3 data.table_1.15.4 FNN_1.1.4
[91] httr_1.4.7 htmlwidgets_1.6.4 uwot_0.2.2 pkgconfig_2.0.3 gtable_0.3.5 registry_0.5-1
[97] ComplexHeatmap_2.20.0 lmtest_0.9-40 htmltools_0.5.8.1 carData_3.0-5 profvis_0.3.8 dotCall64_1.1-1
[103] clue_0.3-65 SeuratObject_5.0.2 scales_1.3.0 png_0.1-8 rstudioapi_0.16.0 reshape2_1.4.4
[109] rjson_0.2.21 coda_0.19-4.1 statnet.common_4.9.0 nlme_3.1-164 cachem_1.1.0 zoo_1.8-12
[115] GlobalOptions_0.1.2 stringr_1.5.1 KernSmooth_2.23-24 parallel_4.4.1 miniUI_0.1.1.1 pillar_1.9.0
[121] grid_4.4.1 vctrs_0.6.5 RANN_2.6.1 urlchecker_1.0.1 promises_1.3.0 ggpubr_0.6.0
[127] car_3.1-2 xtable_1.8-4 cluster_2.1.6 cli_3.6.2 compiler_4.4.1 rlang_1.1.4
[133] crayon_1.5.3 rngtools_1.5.2 future.apply_1.11.2 ggsignif_0.6.4 plyr_1.8.9 fs_1.6.4
[139] stringi_1.8.4 network_1.18.2 viridisLite_0.4.2 deldir_2.0-4 gridBase_0.4-7 BiocParallel_1.38.0
[145] munsell_0.5.1 lazyeval_0.2.2 devtools_2.4.5 spatstat.geom_3.2-9 Matrix_1.7-0 RcppHNSW_0.6.0
[151] patchwork_1.2.0 future_1.33.2 shiny_1.8.1.1 ROCR_1.0-11 broom_1.0.6 memoise_2.0.1
[157] bslib_0.7.0
cellchat <- smoothData(cellchat, PPI.human)
Error in smoothData(cellchat, PPI.human) :
不是所有的is(adj, "matrix") || is(adj, "sparseMatrix")都是TRUE