dynverse
plot_dimred error
It worked before and then got the error since I updated some packages. I seems there is no argument return_other_dimreds for function get_dimred in package dynwrap.
The command I used:
plot_dimred(model)
error:
Error in get_dimred(dataset = trajectory, dimred = dimred, expression_source = expression_source, :
unused argument (return_other_dimreds = TRUE)
Hi @lixin4306ren,
I just merged the devel branch of dynwrap into master. Updating dynwrap should solve your problem.
devtools::install_github("dynverse/dynwrap")
Robrecht
Thanks. I installed the latest dynwrap. However, sometimes I got this error when I set root milestone.
>plot_dimred(model)
>model <- model %>% add_root(root_milestone_id = "1")
> plot_dimred(model)
Coloring by milestone
Using milestone_percentages from trajectory
Error in approx(rel_edge_pos$percentage, rel_edge_pos[[cn]], df$percentage) :
need at least two non-NA values to interpolate
I'm also running into this error.
> model_rooted <- model_slingshot %>% add_root(root_milestone_id = 1)
> plot_dimred(model_rooted, color_cells = "pseudotime", expression_source = dataset)
Pseudotime not provided, will calculate pseudotime from root milestone
> model_rooted <- model_slingshot %>% add_root(root_milestone_id = 4)
> plot_dimred(model_rooted, color_cells = "pseudotime", expression_source = dataset,
plot_trajectory = F)
Pseudotime not provided, will calculate pseudotime from root milestone
Adding the plot_trajectory=F line allows it to plot, but it seems like only one of the branches is being considered in the pseudo-time calculations.
Without it, i run into the same error:
> plot_dimred(model_rooted, color_cells = "pseudotime", expression_source = dataset)
Pseudotime not provided, will calculate pseudotime from root milestone
Error in approx(rel_edge_pos$percentage, rel_edge_pos[[cn]], df$percentage) :
need at least two non-NA values to interpolate
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
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
other attached packages:
[1] dyno_0.1.1 dynwrap_1.1.4 dynplot_1.0.2.9000 dynmethods_1.0.5 dynfeature_1.0.0
[6] shiny_1.4.0 dynguidelines_1.0.0 uwot_0.1.4 Matrix_1.2-17 cytotidyr_0.0.1.100
[11] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3 purrr_0.3.3 readr_1.3.1
[16] tidyr_1.0.0 tibble_2.1.3 ggplot2_3.2.1 tidyverse_1.2.1 sqldf_0.4-11
[21] gsubfn_0.7 proto_1.0.0 CoGAPS_3.4.1 RSQLite_2.1.1
loaded via a namespace (and not attached):
[1] flowWorkspace_3.32.0 GGally_1.4.0 R.methodsS3_1.7.1
[4] GA_3.2 acepack_1.4.1 bit64_0.9-7
[7] knitr_1.26 irlba_2.3.3 DelayedArray_0.10.0
[10] R.utils_2.9.0 data.table_1.12.6 rpart_4.1-15
[13] RCurl_1.95-4.12 generics_0.0.2 flowCore_1.50.0
[16] BiocGenerics_0.30.0 callr_3.3.2 cowplot_1.0.0
[19] usethis_1.5.1 carrier_0.1.0 chron_2.3-54
[22] bit_1.1-14 xml2_1.2.2 lubridate_1.7.4
[25] httpuv_1.5.2 SummarizedExperiment_1.14.1 assertthat_0.2.1
[28] viridis_0.5.1 xfun_0.11 hms_0.5.2
[31] promises_1.1.0 fansi_0.4.0 DEoptimR_1.0-8
[34] dbplyr_1.4.2 caTools_1.17.1.2 readxl_1.3.1
[37] Rgraphviz_2.28.0 igraph_1.2.4.1 DBI_1.0.0
[40] htmlwidgets_1.5.1 reshape_0.8.8 stats4_3.6.1
[43] dyndimred_1.0.2 ellipsis_0.3.0 ks_1.11.5
[46] ggcyto_1.12.0 backports_1.1.5 flowUtils_1.48.0
[49] RcppParallel_4.4.4 vctrs_0.2.0 SingleCellExperiment_1.6.0
[52] Biobase_2.44.0 remotes_2.1.0 withr_2.1.2
[55] ggforce_0.3.1 robustbase_0.93-5 checkmate_1.9.4
[58] prettyunits_1.0.2 mclust_5.4.3 mnormt_1.5-5
[61] cluster_2.0.9 lazyeval_0.2.2 crayon_1.3.4
[64] babelwhale_1.0.1 hdf5r_1.3.0 ellipse_0.4.1
[67] labeling_0.3 pkgconfig_2.0.3 tweenr_1.0.1
[70] GenomeInfoDb_1.20.0 vipor_0.4.5 nlme_3.1-140
[73] pkgload_1.0.2 nnet_7.3-12 devtools_2.2.1
[76] rlang_0.4.2 lifecycle_0.1.0 CytobankAPI_1.3.0
[79] akima_0.6-2 modelr_0.1.5 cellranger_1.1.0
[82] tcltk_3.6.1 rprojroot_1.3-2 polyclip_1.10-0
[85] matrixStats_0.54.0 graph_1.62.0 flowClust_3.22.0
[88] Rhdf5lib_1.6.3 base64enc_0.1-3 processx_3.4.1
[91] viridisLite_0.3.0 bitops_1.0-6 R.oo_1.22.0
[94] KernSmooth_2.23-15 blob_1.2.0 S4Vectors_0.22.1
[97] scales_1.1.0 memoise_1.1.0 magrittr_1.5
[100] plyr_1.8.4 hexbin_1.27.3 gplots_3.0.1.1
[103] gdata_2.18.0 zlibbioc_1.30.0 openCyto_1.22.0
[106] compiler_3.6.1 RColorBrewer_1.1-2 clue_0.3-57
[109] rrcov_1.4-7 cli_1.1.0 XVector_0.24.0
[112] patchwork_0.0.1 ncdfFlow_2.30.0 ps_1.3.0
[115] htmlTable_1.13.2 Formula_1.2-3 MASS_7.3-51.4
[118] tidyselect_0.2.5 stringi_1.4.3 yaml_2.2.0
[121] latticeExtra_0.6-28 ggrepel_0.8.1 grid_3.6.1
[124] tools_3.6.1 parallel_3.6.1 CytoML_1.10.0
[127] rstudioapi_0.10 foreach_1.4.7 foreign_0.8-71
[130] rje_1.10.10 gridExtra_2.3 farver_2.0.1
[133] ggraph_2.0.0 proxyC_0.1.5 digest_0.6.23
[136] dynparam_1.0.0 Rcpp_1.0.3 GenomicRanges_1.36.1
[139] broom_0.5.2 later_1.0.0 shinyWidgets_0.4.9
[142] fda_2.4.8 httr_1.4.1 IDPmisc_1.1.19
[145] flowStats_3.42.0 colorspace_1.4-1 ranger_0.11.2
[148] rvest_0.3.4 XML_3.98-1.19 fs_1.3.1
[151] IRanges_2.18.3 splines_3.6.1 RBGL_1.60.0
[154] graphlayouts_0.5.0 sp_1.3-1 sessioninfo_1.1.1
[157] xtable_1.8-4 jsonlite_1.6 tidygraph_1.1.2
[160] corpcor_1.6.9 zeallot_0.1.0 testthat_2.3.0
[163] R6_2.4.1 RUnit_0.4.32 Hmisc_4.3-0
[166] pillar_1.4.2 htmltools_0.4.0 mime_0.7
[169] glue_1.3.1 fastmap_1.0.1 BiocParallel_1.18.1
[172] codetools_0.2-16 utf8_1.1.4 pkgbuild_1.0.6
[175] pcaPP_1.9-73 mvtnorm_1.0-10 lattice_0.20-38
[178] flowViz_1.48.0 curl_4.2 gtools_3.8.1
[181] shinyjs_1.0 survival_3.1-7 desc_1.2.0
[184] dynutils_1.0.4 munsell_0.5.0 rhdf5_2.28.1
[187] GenomeInfoDbData_1.2.1 iterators_1.0.12 haven_2.1.0
[190] reshape2_1.4.3 gtable_0.3.0
We test th examles under Rsudio as the following command, howerver, it reports errors, we can't find the reason, plot_dimred(example_bifurcating)
errors:
Coloring by milestone
Using milestone_percentages from trajectory
Loading required namespace: RColorBrewer
Error in ggforce::geom_link2():
! Problem while converting geom to grob.
ℹ Error occurred in the 7th layer.
Caused by error in [.data.frame:
! undefined columns selected
Run rlang::last_trace() to see where the error occurred.
