Error/Output interpretation help for demonstration dataset

[allie-burns]

Hello,

First, I enjoyed reading about this tool on bioRxiv and I'm curious to try it out on my own single-nuclear dataset. I've managed to get Augur and sparseMatrixStat installed. Just to test that everything run smoothly, I tried to follow the code in the Demonstration section of the README using the toy dataset that you provide. I'm having a little bit of trouble interpreting the output of calculate_auc in order to figure where the error is coming from.

> augur = calculate_auc(sc_sim,n_threads = 1)
  |                                                                           |   0%, ETA NA
Error: Problem with `mutate()` input `metrics`.
✖ In metric: `roc_auc_custom`
Problem with `summarise()` input `.estimate`.
✖ formal argument "direction" matched by multiple actual arguments
ℹ Input `.estimate` is `metric_fn(...)`.
ℹ Input `metrics` is `pred %>% map(metric_fun)`.

Have you seen something like this before? Is it only a problem with the mutate() and summarise() calls or is this multiple errors?

I appreciate any help and feedback. Please let me know what other information you would need.

Cheers, Allie

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] dplyr_1.0.0  Seurat_3.1.5 Augur_1.0.0 

loaded via a namespace (and not attached):
  [1] nlme_3.1-148            tsne_0.1-3              matrixStats_0.56.0     
  [4] lubridate_1.7.9         RcppAnnoy_0.0.16        RColorBrewer_1.1-2     
  [7] httr_1.4.1              sctransform_0.2.1       tools_3.6.1            
 [10] R6_2.4.1                irlba_2.3.3             rpart_4.1-15           
 [13] KernSmooth_2.23-17      uwot_0.1.8              lazyeval_0.2.2         
 [16] colorspace_1.4-1        yardstick_0.0.7         nnet_7.3-14            
 [19] withr_2.2.0             tidyselect_1.1.0        gridExtra_2.3          
 [22] compiler_3.6.1          glmnet_4.0-2            plotly_4.9.2.1         
 [25] scales_1.1.1            lmtest_0.9-37           ggridges_0.5.2         
 [28] pbapply_1.4-2           rappdirs_0.3.1          stringr_1.4.0          
 [31] digest_0.6.25           pkgconfig_2.0.3         htmltools_0.5.0        
 [34] sparseMatrixStats_1.1.8 MatrixGenerics_1.1.2    htmlwidgets_1.5.1      
 [37] rlang_0.4.7             shape_1.4.4             generics_0.0.2         
 [40] zoo_1.8-8               jsonlite_1.7.0          ica_1.0-2              
 [43] magrittr_1.5            patchwork_1.0.1         Matrix_1.2-18          
 [46] Rcpp_1.0.5              munsell_0.5.0           ape_5.4                
 [49] reticulate_1.16         lifecycle_0.2.0         furrr_0.1.0            
 [52] stringi_1.4.6           pROC_1.16.2             MASS_7.3-51.6          
 [55] Rtsne_0.15              plyr_1.8.6              recipes_0.1.13         
 [58] grid_3.6.1              parallel_3.6.1          listenv_0.8.0          
 [61] ggrepel_0.8.2           crayon_1.3.4            lattice_0.20-41        
 [64] cowplot_1.0.0           splines_3.6.1           pillar_1.4.6           
 [67] igraph_1.2.5            future.apply_1.6.0      reshape2_1.4.4         
 [70] codetools_0.2-16        parsnip_0.1.2           leiden_0.3.3           
 [73] glue_1.4.1              rsample_0.0.7           tester_0.1.7           
 [76] data.table_1.12.8       foreach_1.5.0           vctrs_0.3.1            
 [79] png_0.1-7               gtable_0.3.0            RANN_2.6.1             
 [82] purrr_0.3.4             tidyr_1.1.0             future_1.18.0          
 [85] ggplot2_3.3.2           gower_0.2.2             rsvd_1.0.3             
 [88] prodlim_2019.11.13      class_7.3-17            survival_3.2-3         
 [91] viridisLite_0.3.0       timeDate_3043.102       tibble_3.0.3           
 [94] iterators_1.0.12        pbmcapply_1.5.0         cluster_2.1.0          
 [97] lava_1.6.7              globals_0.12.5          fitdistrplus_1.1-1     
[100] ellipsis_0.3.1          ROCR_1.0-11             ipred_0.9-9  

[skinnider]

Thanks for this note @allie-burns - the error had to do with some changes that have been made to the yardstick package (we had only ever tested with v0.0.4 but I see your clean install has v0.0.7). I just pushed a fix to master that updates Augur to work with the most recent release of yardstick. Hope this solves your problem, let me know if you are still getting an error.

[allie-burns]

Thanks for the update @skinnider. It's working now!