Entering edit mode
Hello,
I am getting an error when calling plot3d.SlingshotDataSet as indicated in the below code. I'm also including traceback, sessionInfo and valid information are below. Can you advise? Thanks,
Elisabetta
library(tidyverse)
library(Seurat)
library(slingshot)
library(scales)
library(RColorBrewer)
library(rgl)
epi <- readRDS('epi.rds')
epi
## An object of class Seurat
## 35391 features across 26008 samples within 2 assays
## Active assay: integrated (4338 features, 4338 variable features)
## 1 other assay present: RNA
## 3 dimensional reductions calculated: pca, umap, tsne
sling3 <- slingshot(Embeddings(epi, "pca")[,1:3], clusterLabels=Idents(epi), start.clus='Stem')
sling3
## class: PseudotimeOrdering
## dim: 26008 4
## metadata(4): lineages mst slingParams curves
## pathStats(2): pseudotime weights
## cellnames(26008): A_AAGTGAACACTTTATC A_AAGTGAACAGTGGCTC ... D_TTTGTTGTCGGCATTA
## D_TTTGTTGTCTCAATCT
## cellData names(2): reducedDim clusterLabels
## pathnames(4): Lineage1 Lineage2 Lineage3 Lineage4
## pathData names(0):
plot3d.SlingshotDataSet(sling3, type='l')
## Error in (function (classes, fdef, mtable) :
## unable to find an inherited method for function ‘reducedDim’ for signature ‘"PseudotimeOrdering", "missing"’
traceback()
## 5: stop(gettextf("unable to find an inherited method for function %s for signature %s",
## sQuote(fdef@generic), sQuote(cnames)), domain = NA)
## 4: (function (classes, fdef, mtable)
## {
## methods <- .findInheritedMethods(classes, fdef, mtable)
## if (length(methods) == 1L)
## return(methods[[1L]])
## else if (length(methods) == 0L) {
## cnames <- paste0("\"", vapply(classes, as.character,
## ""), "\"", collapse = ", ")
## stop(gettextf("unable to find an inherited method for function %s for signature %s",
## sQuote(fdef@generic), sQuote(cnames)), domain = NA)
## }
## else stop("Internal error in finding inherited methods; didn't return a unique method",
## domain = NA)
## })(list(structure("PseudotimeOrdering", package = "TrajectoryUtils"),
## structure("missing", package = "methods")), new("standardGeneric",
## .Data = function (x, type, ...)
## standardGeneric("reducedDim"), generic = structure("reducedDim", package = "SingleCellExperiment"),
## package = "SingleCellExperiment", group = list(), valueClass = character(0),
## signature = c("x", "type"), default = NULL, skeleton = (function (x,
## type, ...)
## ...
## 3: reducedDim(x)
## 2: nrow(reducedDim(x))
## 1: plot3d.SlingshotDataSet(sling3, type = "l")
sessionInfo()
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19044)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
## [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
## [5] LC_TIME=English_United States.1252
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] rgl_0.108.3.2 RColorBrewer_1.1-3 scales_1.2.0
## [4] slingshot_2.0.0 TrajectoryUtils_1.0.0 SingleCellExperiment_1.14.1
## [7] SummarizedExperiment_1.22.0 Biobase_2.52.0 GenomicRanges_1.44.0
## [10] GenomeInfoDb_1.28.4 IRanges_2.26.0 S4Vectors_0.30.2
## [13] BiocGenerics_0.38.0 MatrixGenerics_1.4.3 matrixStats_0.62.0
## [16] princurve_2.1.6 sp_1.4-7 SeuratObject_4.1.0
## [19] Seurat_4.1.1 forcats_0.5.1 stringr_1.4.0
## [22] dplyr_1.0.9 purrr_0.3.4 readr_2.1.2
## [25] tidyr_1.2.0 tibble_3.1.7 ggplot2_3.3.6
## [28] tidyverse_1.3.1
##
## loaded via a namespace (and not attached):
## [1] readxl_1.4.0 backports_1.4.1 plyr_1.8.7 igraph_1.3.1
## [5] lazyeval_0.2.2 splines_4.1.2 listenv_0.8.0 scattermore_0.8
## [9] digest_0.6.29 htmltools_0.5.2 fansi_1.0.3 magrittr_2.0.3
## [13] tensor_1.5 cluster_2.1.3 ROCR_1.0-11 tzdb_0.3.0
## [17] globals_0.15.0 modelr_0.1.8 spatstat.sparse_2.1-1 colorspace_2.0-3
## [21] rvest_1.0.2 ggrepel_0.9.1 haven_2.5.0 xfun_0.31
## [25] RCurl_1.98-1.6 crayon_1.5.1 jsonlite_1.8.0 progressr_0.10.1
## [29] spatstat.data_2.2-0 survival_3.3-1 zoo_1.8-10 glue_1.6.2
## [33] polyclip_1.10-0 gtable_0.3.0 zlibbioc_1.38.0 XVector_0.32.0
## [37] leiden_0.4.2 DelayedArray_0.18.0 future.apply_1.9.0 abind_1.4-5
## [41] DBI_1.1.2 spatstat.random_2.2-0 miniUI_0.1.1.1 Rcpp_1.0.8.3
## [45] viridisLite_0.4.0 xtable_1.8-4 reticulate_1.25 spatstat.core_2.4-4
## [49] htmlwidgets_1.5.4 httr_1.4.3 ellipsis_0.3.2 ica_1.0-2
## [53] pkgconfig_2.0.3 uwot_0.1.11 dbplyr_2.2.0 deldir_1.0-6
## [57] utf8_1.2.2 tidyselect_1.1.2 rlang_1.0.2 reshape2_1.4.4
## [61] later_1.3.0 munsell_0.5.0 cellranger_1.1.0 tools_4.1.2
## [65] cli_3.3.0 generics_0.1.2 broom_0.8.0 ggridges_0.5.3
## [69] fastmap_1.1.0 goftest_1.2-3 knitr_1.39 fs_1.5.2
## [73] fitdistrplus_1.1-8 RANN_2.6.1 pbapply_1.5-0 future_1.26.1
## [77] nlme_3.1-157 mime_0.12 xml2_1.3.3 compiler_4.1.2
## [81] rstudioapi_0.13 plotly_4.10.0 png_0.1-7 spatstat.utils_2.3-1
## [85] reprex_2.0.1 stringi_1.7.6 rgeos_0.5-9 lattice_0.20-45
## [89] Matrix_1.4-1 vctrs_0.4.1 pillar_1.7.0 lifecycle_1.0.1
## [93] BiocManager_1.30.18 spatstat.geom_2.4-0 lmtest_0.9-40 RcppAnnoy_0.0.19
## [97] bitops_1.0-7 data.table_1.14.2 cowplot_1.1.1 irlba_2.3.5
## [101] httpuv_1.6.5 patchwork_1.1.1 R6_2.5.1 promises_1.2.0.1
## [105] KernSmooth_2.23-20 gridExtra_2.3 parallelly_1.32.0 codetools_0.2-18
## [109] MASS_7.3-57 assertthat_0.2.1 withr_2.5.0 sctransform_0.3.3
## [113] GenomeInfoDbData_1.2.6 mgcv_1.8-40 hms_1.1.1 grid_4.1.2
## [117] rpart_4.1.16 Rtsne_0.16 shiny_1.7.1 lubridate_1.8.0
BiocManager::valid()
## 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
##
## replacement repositories:
## CRAN: https://cran.rstudio.com/
##
##
## * sessionInfo()
##
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19044)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
## [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
## [5] LC_TIME=English_United States.1252
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] BiocManager_1.30.18 compiler_4.1.2 tools_4.1.2
##
## Bioconductor version '3.13'
##
## * 2 packages out-of-date
## * 0 packages too new
##
## create a valid installation with
##
## BiocManager::install(c(
## "restfulr", "sp"
## ), update = TRUE, ask = FALSE)
##
## more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
##
## Warning message:
## 2 packages out-of-date; 0 packages too new
Ahhh, yes that was the problem, thanks! Elisabetta
Hi please i am encountering similar issue how did you fix it. Here is the code:
Run Slingshot
p3.neuron.sds <- slingshot(Embeddings(object=p3.moe.neuron.integrated, "pca")[,1:50], clusterLabels = p3.moe.neuron.integrated@active.ident, start.clus = "GBC", end.clus = "mOSN", stretch = 0)
And i am trying to plot the result
svglite(filename = paste0(paper_images,"p3.slingshot.centroids.cell_type.svg"),width=10,height=10) plot(reducedDim(p3.neuron.sds),col=p3.neuron.celltype.col,pch=16,cex=0.5) lines(p3.neuron.sds,lwd=2,type='lineages',col='black') legend("topright",legend=levels(p3.moe.neuron.integrated@active.ident), col=p3.moe.neuron.colors.cell_type,pch=16,bty='n') invisible(dev.off())
i keep getting this error message
This issue has been addressed on GitHub.