plot_dimred() error: Must supply a symbol or a string as argument

[pawelqs]

Hi!

Thanks for developping of this awesome package! Could you help me to resolve the following error?

This is the code that I used and the error message that I receive:

dataset <- wrap_expression(
    counts = t(ur_counts),
    expression = t(ur_normalized)
  ) %>%
  add_grouping(ur$seurat_clusters)

model <- infer_trajectory(dataset, "slingshot")

head(get_dimred(model), 5)
#                       comp_1    comp_2     comp_3
# AAACCCAAGTAGCTCT-1   6.274450 -2.478266 -0.4647137
# AAACCCACACCGAATT-1  -1.657088  3.400508 -4.0767709
# AAACCCATCACGTCCT-1  -3.980528  1.925050 -1.8245143
# AAACGAACACCTAAAC-1   3.819722 -3.118579  0.4000323
# AAACGAACAGAACCGA-1 -14.138137  5.310757  3.9100437

plot_dimred(model)
# Coloring by milestone
# Using milestone_percentages from trajectory
# Error: Must supply a symbol or a string as argument
# Run `rlang::last_error()` to see where the error occurred.

And further info:

rlang::last_error()
# <error/rlang_error>
# Must supply a symbol or a string as argument
# Backtrace:
#  1. dynplot::plot_dimred(model)
#  7. tidyr:::gather.data.frame(...)
#  10. tidyr:::ensym2(key)
# Run `rlang::last_trace()` to see the full context.

rlang::last_trace()
# <error/rlang_error>
# Must supply a symbol or a string as argument
# Backtrace:
#     x
#  1. +-dynplot::plot_dimred(model)
#  2. | \-dynplot:::project_waypoints_coloured(...)
#  3. |   \-`%>%`(...)
#  4. +-dplyr::summarise(...)
#  5. +-dplyr::group_by(., .data$from, .data$to, .data$comp_name)
#  6. +-tidyr::gather(., .data$comp_name, .data$comp_value, starts_with("comp_"))
#  7. \-tidyr:::gather.data.frame(...)
#  8.   +-rlang::as_string(ensym2(key))
#  9.   | \-rlang::is_string(x)
# 10.   \-tidyr:::ensym2(key)

sessionInfo()
# R version 4.0.3 (2020-10-10)
# Platform: x86_64-w64-mingw32/x64 (64-bit)
# Running under: Windows 10 x64 (build 19042)

...
# other attached packages:
#  [1] shiny_1.6.0                 dyno_0.1.2                  dynwrap_1.2.2              
#  [4] dynplot_1.1.0               dynmethods_1.0.5            dynguidelines_1.0.1        
#  [7] dynfeature_1.0.0            ggplotify_0.0.5             ggbeeswarm_0.6.0
....

What can be wrong?

Best,
Paweł

[rcannood]

Hi Paweł!

Thanks for reporting this issue. It seems a small bug snuck into the code during the last release.

By installing the dynplot@devel branch, you should now be able to run the following code:

library(dyno)
library(tidyverse)

ur_counts <- matrix(runif(1000), nrow = 40)
rownames(ur_counts) <- paste0("cell_", seq_len(nrow(ur_counts)))
colnames(ur_counts) <- paste0("gene_", seq_len(ncol(ur_counts)))

ur_normalized <- ur_counts
ur <- list(seurat_clusters = round(ur_counts[,1]*10))
  
dataset <- wrap_expression(
  counts = t(ur_counts),
  expression = t(ur_normalized)
) %>%
  add_grouping(ur$seurat_clusters)

model <- infer_trajectory(dataset, tislingshot::ti_slingshot())

head(get_dimred(model), 5)

plot_dimred(model)

Can you run devtools::install_github("dynverse/dynplot@devel") to confirm that it has been solved?

Kind regards,
Robrecht

[pawelqs]

Yes, it works now. Thank you!

A am a little bit worried now about the trajectory detected in the data. Why is it so short?

[Bio-data-tricks]

Hi Pawel125,

I have the same issue with my data. The same code works well two weeks ago.

Nicolas

[rcannood]

Hey Nicolas, Can you provide me with a reproducible example? Thanks Robrecht

…

On Sun, 27 Jun 2021, 11:44 n.GoFF, ***@***.***> wrote: Hi Pawel125, I have the same issue with my data. The same code works well two weeks ago. [image: Capture] <https://user-images.githubusercontent.com/25744843/123540009-f6968000-d73c-11eb-9b27-11fd04bf9e2d.PNG> Nicolas — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#54 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEHFKTQU2AY37PI64BDBCDTU3XHTANCNFSM47HTPOPA> .

[Bio-data-tricks]

Hi Robrecht,

Here is the code,

dataset <- wrap_expression(
  counts = X,
  expression = X,
  dimred_acp = dyndimred::dimred_pca(X))

model_paga <- infer_trajectory(
  dataset = dataset,
  method = dynmethods::ti_projected_paga(filter_features = FALSE, 
                                         n_neighbors =15L,
                                         resolution = 1L,
                                         embedding_type = "umap"),
  verbose = FALSE)

plot_dimred(model_paga, grouping = group_onto_nearest_milestones(model_paga), label_milestones=TRUE)

I have just updated the packages dynmethods, dynplot,dyno with devtools::install_github("dynverse/dynplot")
Moreover it seems that figures have a different appearance, less resolute.

R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252

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

other attached packages:
[1] RColorBrewer_1.1-2 RCurl_1.98-1.3 knitr_1.33
[4] viridis_0.6.1 viridisLite_0.4.0 arrow_4.0.1
[7] feather_0.3.5 ggthemes_4.2.4 plot3D_1.4
[10] reshape_0.8.8 Matrix_1.3-4 svglite_2.0.0
[13] readxl_1.3.1 dyno_0.1.2 dynwrap_1.2.2
[16] dynplot_1.1.1 dynmethods_1.0.5.9000 dynguidelines_1.0.1
[19] dynfeature_1.0.0 forcats_0.5.1 stringr_1.4.0
[22] dplyr_1.0.6 purrr_0.3.4 readr_1.4.0
[25] tidyr_1.1.3 tibble_3.1.2 ggplot2_3.3.5
[28] tidyverse_1.3.1

loaded via a namespace (and not attached):
[1] uuid_0.1-4 backports_1.2.1 dyndimred_1.0.4
[4] systemfonts_1.0.2 babelwhale_1.0.3 plyr_1.8.6
[7] igraph_1.2.6 repr_1.1.3 proxyC_0.2.0
[10] usethis_2.0.1 digest_0.6.27 foreach_1.5.1
[13] htmltools_0.5.1.1 fansi_0.5.0 magrittr_2.0.1
[16] memoise_2.0.0 carrier_0.1.0 remotes_2.4.0
[19] graphlayouts_0.7.1 modelr_0.1.8 RcppParallel_5.1.4
[22] dynutils_1.0.6 prettyunits_1.1.1 colorspace_2.0-1
[25] rvest_1.0.0 ggrepel_0.9.1 haven_2.4.1
[28] xfun_0.24 tcltk_4.1.0 callr_3.7.0
[31] crayon_1.4.1 jsonlite_1.7.2 iterators_1.0.13
[34] glue_1.4.2 polyclip_1.10-0 gtable_0.3.0
[37] pkgbuild_1.2.0 dynparam_1.0.2 scales_1.1.1
[40] DBI_1.1.1 Rcpp_1.0.6 xtable_1.8-4
[43] bit_4.0.4 httr_1.4.2 ellipsis_0.3.2
[46] pkgconfig_2.0.3 farver_2.1.0 dbplyr_2.1.1
[49] utf8_1.2.1 labeling_0.4.2 tidyselect_1.1.1
[52] rlang_0.4.11 reshape2_1.4.4 later_1.2.0
[55] munsell_0.5.0 cellranger_1.1.0 tools_4.1.0
[58] cachem_1.0.5 cli_2.5.0 generics_0.1.0
[61] ranger_0.12.1 devtools_2.4.2 broom_0.7.7
[64] evaluate_0.14 fastmap_1.1.0 yaml_2.2.1
[67] processx_3.5.2 bit64_4.0.5 fs_1.5.0
[70] tidygraph_1.2.0 lmds_0.1.0 ggraph_2.0.5
[73] mime_0.10 GA_3.2.1 xml2_1.3.2
[76] hdf5r_1.3.3 compiler_4.1.0 rstudioapi_0.13
[79] curl_4.3.1 testthat_3.0.2 reprex_2.0.0
[82] tweenr_1.0.2 stringi_1.6.2 ps_1.6.0
[85] desc_1.3.0 lattice_0.20-44 IRdisplay_1.0
[88] vctrs_0.3.8 pillar_1.6.1 lifecycle_1.0.0
[91] bitops_1.0-7 irlba_2.3.3 httpuv_1.6.1
[94] patchwork_1.1.0.9000 R6_2.5.0 promises_1.2.0.1
[97] gridExtra_2.3 sessioninfo_1.1.1 codetools_0.2-18
[100] MASS_7.3-54 assertthat_0.2.1 pkgload_1.2.1
[103] rprojroot_2.0.2 withr_2.4.2 hms_1.1.0
[106] grid_4.1.0 IRkernel_1.2 misc3d_0.9-0
[109] pbdZMQ_0.3-5 ggforce_0.3.3 shiny_1.6.0
[112] lubridate_1.7.10 base64enc_0.1-3

Thanks

Nicolas

[rcannood]

Hi @Bio-data-tricks @pawel125 ,

Can you try reinstalling dynplot? (devtools::install_github("dynverse/dynplot@devel")). The issue should have been resolved.

If you can confirm the issue has been solved, I'll submit an update for dynplot to CRAN.

Kind regards,
Robrecht

[Bio-data-tricks]

Thank you Robrecht, issue solved !

[Bio-data-tricks]

Robrecht,

Have you an idea why I've a bad labels positioning in this umap embedding (doing after the paga trajectory inference) ?

Nicolas

[NaijIuc]

Hi Robrecht,

I have the same issue. But no matter how I tried following your suggestions above, I cannot get the program run. The followings are my code, and could you please take a look?

I have tried with devtools::install_github("dynverse/dynplot@devel")

Thanks for your time

dat <- readRDS("mySeuratProject")

dataset <- wrap_expression(
  counts = t(dat@assays$RNA@counts),
  expression = t(dat@assays$RNA@data)
) %>%
  add_grouping(dat$finClu)

guidelines <- guidelines_shiny(dataset)
methods_selected <- guidelines$methods_selected

model <- infer_trajectory(dataset, methods_selected[1])

model <- infer_trajectory(dataset, dynmethods::ti_slingshot())

plot_dimred(
  model, 
  expression_source = dataset$expression,
  grouping = dataset$grouping
)
# The outcome for both methods above have the same error:

Coloring by grouping
Error: Must supply a symbol or a string as argument
Run `rlang::last_error()` to see where the error occurred.

> rlang::last_error()
<error/rlang_error>
Must supply a symbol or a string as argument
Backtrace:
  1. dynplot::plot_dimred(...)
  7. tidyr:::gather.data.frame(...)
 10. tidyr:::ensym2(key)
Run `rlang::last_trace()` to see the full context.
> rlang::last_trace()
<error/rlang_error>
Must supply a symbol or a string as argument
Backtrace:
     x
  1. +-dynplot::plot_dimred(...)
  2. | \-dynplot:::project_waypoints_coloured(...)
  3. |   \-`%>%`(...)
  4. +-dplyr::summarise(...)
  5. +-dplyr::group_by(., .data$from, .data$to, .data$comp_name)
  6. +-tidyr::gather(., .data$comp_name, .data$comp_value, starts_with("comp_"))
  7. \-tidyr:::gather.data.frame(...)
  8.   +-rlang::as_string(ensym2(key))
  9.   | \-rlang::is_string(x)
 10.   \-tidyr:::ensym2(key)
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

[cdsoria]

Hi @rcannood. Thank you for such useful tools. Unfortunately, I have the same issue as @NaijIuc. I also installed the devtools::install_github("dynverse/dynplot@devel") and followed the example you have online. Thank you

[NaijIuc]

Hi @rcannood. Thank you for such useful tools. Unfortunately, I have the same issue as @NaijIuc. I also installed the devtools::install_github("dynverse/dynplot@devel") and followed the example you have online. Thank you

You can try to change R version like 3.6, 4.05, 4.10 etc.. I have no clue why I finally can let it run, but I am highly doubting that is relevant to R version.

[cdsoria]

Hi @rcannood. Thank you for such useful tools. Unfortunately, I have the same issue as @NaijIuc. I also installed the devtools::install_github("dynverse/dynplot@devel") and followed the example you have online. Thank you

You can try to change R version like 3.6, 4.05, 4.10 etc.. I have no clue why I finally can let it run, but I am highly doubting that is relevant to R version.

Thanks you. Will try

[royfrancis]

I was getting the same error with my data and even with the example from quick-start. Updated to devel version of dynplot and still had the error. I restarted my R session and tried again and it worked. So those getting this error, try again in a clean environment. Probably a conflicting function somewhere.

You can run the short reproducible example below to be sure that it works and it's not your data or the version of dynplot.

library(dyno)
#> Loading required package: dynfeature
#> Loading required package: dynguidelines
#> Loading required package: dynmethods
#> Loading required package: dynplot
#> Loading required package: dynwrap
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

data("fibroblast_reprogramming_treutlein")

dataset <- wrap_expression(
  counts = fibroblast_reprogramming_treutlein$counts,
  expression = fibroblast_reprogramming_treutlein$expression
)

model <- infer_trajectory(dataset, "slingshot")
#> Loading required namespace: hdf5r
model <- model %>% add_dimred(dyndimred::dimred_mds, expression_source = dataset$expression)
plot_dimred(
  model, 
  expression_source = dataset$expression, 
  grouping = fibroblast_reprogramming_treutlein$grouping
)
#> Coloring by grouping
#> Loading required namespace: RColorBrewer

^{Created on 2021-08-12 by the reprex package (v2.0.1)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.1.0 (2021-05-18)
#>  os       Ubuntu 20.04.2 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_GB:en                    
#>  collate  en_GB.UTF-8                 
#>  ctype    en_GB.UTF-8                 
#>  tz       Europe/Stockholm            
#>  date     2021-08-12                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package       * version date       lib source                                 
#>  assertthat      0.2.1   2019-03-21 [1] CRAN (R 4.1.0)                         
#>  babelwhale      1.0.3   2021-06-25 [1] CRAN (R 4.1.0)                         
#>  bit             4.0.4   2020-08-04 [1] CRAN (R 4.1.0)                         
#>  bit64           4.0.5   2020-08-30 [1] CRAN (R 4.1.0)                         
#>  carrier         0.1.0   2018-10-16 [1] CRAN (R 4.1.0)                         
#>  cli             3.0.1   2021-07-17 [1] CRAN (R 4.1.0)                         
#>  codetools       0.2-18  2020-11-04 [1] CRAN (R 4.1.0)                         
#>  colorspace      2.0-2   2021-06-24 [1] CRAN (R 4.1.0)                         
#>  crayon          1.4.1   2021-02-08 [1] CRAN (R 4.1.0)                         
#>  curl            4.3.2   2021-06-23 [1] CRAN (R 4.1.0)                         
#>  DBI             1.1.1   2021-01-15 [1] CRAN (R 4.1.0)                         
#>  desc            1.3.0   2021-03-05 [1] CRAN (R 4.1.0)                         
#>  digest          0.6.27  2020-10-24 [1] CRAN (R 4.1.0)                         
#>  dplyr         * 1.0.7   2021-06-18 [1] CRAN (R 4.1.0)                         
#>  dyndimred       1.0.4   2021-03-23 [1] CRAN (R 4.1.0)                         
#>  dynfeature    * 1.0.0   2021-08-12 [1] Github (dynverse/dynfeature@62981ce)   
#>  dynguidelines * 1.0.1   2021-08-12 [1] Github (dynverse/dynguidelines@57f2da7)
#>  dynmethods    * 1.0.5   2021-08-12 [1] Github (dynverse/dynmethods@53c6d1d)   
#>  dyno          * 0.1.2   2021-08-12 [1] Github (dynverse/dyno@c461023)         
#>  dynparam        1.0.2   2021-01-04 [1] CRAN (R 4.1.0)                         
#>  dynplot       * 1.1.1   2021-08-12 [1] Github (dynverse/dynplot@8fff437)      
#>  dynutils        1.0.6   2021-03-22 [1] CRAN (R 4.1.0)                         
#>  dynwrap       * 1.2.2   2021-08-12 [1] Github (dynverse/dynwrap@250758b)      
#>  ellipsis        0.3.2   2021-04-29 [1] CRAN (R 4.1.0)                         
#>  evaluate        0.14    2019-05-28 [1] CRAN (R 4.1.0)                         
#>  fansi           0.5.0   2021-05-25 [1] CRAN (R 4.1.0)                         
#>  farver          2.1.0   2021-02-28 [1] CRAN (R 4.1.0)                         
#>  fastmap         1.1.0   2021-01-25 [1] CRAN (R 4.1.0)                         
#>  foreach         1.5.1   2020-10-15 [1] CRAN (R 4.1.0)                         
#>  fs              1.5.0   2020-07-31 [1] CRAN (R 4.1.0)                         
#>  GA              3.2.1   2021-04-21 [1] CRAN (R 4.1.0)                         
#>  generics        0.1.0   2020-10-31 [1] CRAN (R 4.1.0)                         
#>  ggforce         0.3.3   2021-03-05 [1] CRAN (R 4.1.0)                         
#>  ggplot2         3.3.5   2021-06-25 [1] CRAN (R 4.1.0)                         
#>  ggraph          2.0.5   2021-02-23 [1] CRAN (R 4.1.0)                         
#>  ggrepel         0.9.1   2021-01-15 [1] CRAN (R 4.1.0)                         
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#>  gridExtra       2.3     2017-09-09 [1] CRAN (R 4.1.0)                         
#>  gtable          0.3.0   2019-03-25 [1] CRAN (R 4.1.0)                         
#>  hdf5r           1.3.3   2020-08-18 [1] CRAN (R 4.1.0)                         
#>  highr           0.9     2021-04-16 [1] CRAN (R 4.1.0)                         
#>  hms             1.1.0   2021-05-17 [1] CRAN (R 4.1.0)                         
#>  htmltools       0.5.1.1 2021-01-22 [1] CRAN (R 4.1.0)                         
#>  httpuv          1.6.1   2021-05-07 [1] CRAN (R 4.1.0)                         
#>  httr            1.4.2   2020-07-20 [1] CRAN (R 4.1.0)                         
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#>  knitr           1.33    2021-04-24 [1] CRAN (R 4.1.0)                         
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#>  later           1.2.0   2021-04-23 [1] CRAN (R 4.1.0)                         
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#>  lmds            0.1.0   2019-09-27 [1] CRAN (R 4.1.0)                         
#>  magrittr        2.0.1   2020-11-17 [1] CRAN (R 4.1.0)                         
#>  MASS            7.3-54  2021-05-03 [1] CRAN (R 4.1.0)                         
#>  Matrix          1.3-4   2021-06-01 [1] CRAN (R 4.1.0)                         
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#>  rlang           0.4.11  2021-04-30 [1] CRAN (R 4.1.0)                         
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#> [1] /home/roy/miniconda3/envs/r-4.1/lib/R/library

[Bio-data-tricks]

Hi Everyone,

My figures have a different appearance, less resolute as described in the previous comments (with R4.0, R4.1, R3.5)

Have you an idea please ?

Nicolas