Error in plot_dimred function

[Eomesodermin]

I keep getting this error and am unable to resolve it.

I have tried plotting different trajectories and other arguments.

I have also tried both the most up to date version and previous versions of dynutils and the dyno package.

dynplot::plot_dimred(slingshot.total, color_cells = "pseudotime")

Error: 'manhattan_distance' is not an exported object from 'namespace:dynutils'

sessionInfo()

R version 3.5.3 (2019-03-11) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.3

Matrix products: default BLAS: >/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

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

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

other attached packages: [1] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.0.1 purrr_0.3.2 readr_1.3.1 tidyr_0.8.3
[7] tibble_2.1.1 tidyverse_1.2.1 dynutils_1.0.3 dyno_0.1.1 dynwrap_1.0.1 >dynplot_1.0.0.9000 [13] dynmethods_1.0.1 dynguidelines_1.0.0 dynfeature_1.0.0 Seurat_2.3.4 Matrix_1.2-17 >cowplot_0.9.4
[19] ggplot2_3.1.1

loaded via a namespace (and not attached): [1] utf8_1.1.4 reticulate_1.12 R.utils_2.8.0 tidyselect_0.2.5 htmlwidgets_1.3 >grid_3.5.3
[7] trimcluster_0.1-2.1 ranger_0.11.2 Rtsne_0.15 devtools_2.0.2 dyntoy_0.9.9 >munsell_0.5.0
[13] codetools_0.2-16 ica_1.0-2 withr_2.1.2 colorspace_1.4-1 knitr_1.22 >rstudioapi_0.10
[19] stats4_3.5.3 ROCR_1.0-7 robustbase_0.93-4 dtw_1.20-1 gbRd_0.4-11 >labeling_0.3
[25] Rdpack_0.11-0 lars_1.2 polyclip_1.10-0 bit64_0.9-7 farver_1.1.0 >rprojroot_1.3-2
[31] generics_0.0.2 xfun_0.6 diptest_0.75-7 R6_2.4.0 GA_3.2 pdist_1.2
[37] hdf5r_1.2.0 flexmix_2.3-15 bitops_1.0-6 assertthat_0.2.1 promises_1.0.1 SDMTools_1.1-221.1
[43] scales_1.0.0 ggraph_1.0.2 nnet_7.3-12 gtable_0.3.0 babelwhale_0.0.0.9000 npsurv_0.4-0
[49] processx_3.3.0 tidygraph_1.1.2 rlang_0.3.4 akima_0.6-2 splines_3.5.3 lazyeval_0.2.2
[55] acepack_1.4.1 hexbin_1.27.2 broom_0.5.2 checkmate_1.9.3 modelr_0.1.4 BiocManager_1.30.4
[61] yaml_2.2.0 reshape2_1.4.3 backports_1.1.4 httpuv_1.5.1 Hmisc_4.2-0 tools_3.5.3
[67] usethis_1.5.0 gplots_3.0.1.1 RColorBrewer_1.1-2 proxy_0.4-23 sessioninfo_1.1.1 ggridges_0.5.1
[73] Rcpp_1.0.1 plyr_1.8.4 base64enc_0.1-3 ps_1.3.0 prettyunits_1.0.2 rpart_4.1-15
[79] pbapply_1.4-0 viridis_0.5.1 dynparam_1.0.0 zoo_1.8-5 haven_2.1.0 ggrepel_0.8.0
[85] cluster_2.0.9 fs_1.3.0 magrittr_1.5 RSpectra_0.14-0 data.table_1.12.2 carrier_0.1.0
[91] lmtest_0.9-37 RANN_2.6.1 mvtnorm_1.0-10 fitdistrplus_1.0-14 pkgload_1.0.2 hms_0.4.2
[97] patchwork_0.0.1 lsei_1.2-0 mime_0.6 xtable_1.8-4 readxl_1.3.1 mclust_5.4.3
[103] gridExtra_2.3 testthat_2.1.1 compiler_3.5.3 KernSmooth_2.23-15 crayon_1.3.4 rje_1.9
[109] R.oo_1.22.0 htmltools_0.3.6 proxyC_0.1.3 segmented_0.5-3.0 later_0.8.0 Formula_1.2-3
[115] snow_0.4-3 RcppParallel_4.4.2 lubridate_1.7.4 tweenr_1.0.1 MASS_7.3-51.4 fpc_2.1-11.1
[121] cli_1.1.0 R.methodsS3_1.7.1 gdata_2.18.0 parallel_3.5.3 metap_1.1 igraph_1.2.4.1
[127] pkgconfig_2.0.2 dyneval_0.9.9 sp_1.3-1 foreign_0.8-71 xml2_1.2.0 foreach_1.4.4
[133] vipor_0.4.5 rvest_0.3.3 bibtex_0.4.2 callr_3.2.0 digest_0.6.18 dyndimred_1.0.1
[139] RcppAnnoy_0.0.11 tsne_0.1-3 cellranger_1.1.0 htmlTable_1.13.1 uwot_0.1.3 curl_3.3
[145] kernlab_0.9-27 shiny_1.3.2 gtools_3.8.1 modeltools_0.2-22 nlme_3.1-139 jsonlite_1.6
[151] fansi_0.4.0 desc_1.2.0 viridisLite_0.3.0 pillar_1.3.1 lattice_0.20-38 shades_1.3.1
[157] httr_1.4.0 DEoptimR_1.0-8 pkgbuild_1.0.3 survival_2.44-1.1 glue_1.3.1 remotes_2.0.4
[163] FNN_1.1.3 png_0.1-7 prabclus_2.2-7 iterators_1.0.10 bit_1.1-14 ggforce_0.2.2
[169] class_7.3-15 stringi_1.4.3 mixtools_1.1.0 doSNOW_1.0.16 latticeExtra_0.6-28 caTools_1.17.1.2
[175] memoise_1.1.0 irlba_2.3.3 ape_5.3

[rcannood]

Hello Eomesodermin,

Most likely you have an outdated version of dynplot installed. Could you try updating dynplot? (devtools::install_github("dynverse/dynplot"))

Kind regards, Robrecht

[rcannood]

Closing this issue since it is probably already fixed. Feel free to respond if it is not.