plot_dimred error

[lixin4306ren]

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)

[rcannood]

Hi @lixin4306ren,

I just merged the devel branch of dynwrap into master. Updating dynwrap should solve your problem.

devtools::install_github("dynverse/dynwrap")

Robrecht

[lixin4306ren]

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

[bjreisman]

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     

[Atvar2]

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.

[Joanexee]

Got the same undefined columns selected error with example data