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microbiome / miaViz

Microbiome Analysis Plotting and Visualization
https://microbiome.github.io/miaViz
Artistic License 2.0
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Error in .density_plotter(density_data = density_data, layout = layout, : object 'angle.x.test' not found #146

Closed RiboRings closed 3 months ago

RiboRings commented 3 months ago

Hi! I am getting an error when I use plotAbundanceDensity with point or jitter layout and flipped axes. Working with latest miaViz version. Below is a minimal working example.

library(miaViz)
library(mia)

# This works
plotAbundanceDensity(tse, flipped = TRUE, layout = "density")

# This does not work
plotAbundanceDensity(tse, flipped = TRUE, layout = "point")
> Error in .density_plotter(density_data = density_data, layout = layout,  : 
> object 'angle.x.test' not found

# This does not work
plotAbundanceDensity(tse, flipped = TRUE, layout = "jitter")
> Error in .density_plotter(density_data = density_data, layout = layout,  : 
> object 'angle.x.test' not found
RiboRings commented 3 months ago

Session info:

R Under development (unstable) (2024-03-20 r86162)
Platform: x86_64-apple-darwin20
Running under: macOS Big Sur 11.7.10

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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

time zone: Asia/Jerusalem
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets 
[7] methods   base     

other attached packages:
 [1] miaViz_1.13.8                   ggraph_2.2.1                   
 [3] ggplot2_3.5.1                   mia_1.13.34                    
 [5] MultiAssayExperiment_1.31.4     TreeSummarizedExperiment_2.13.0
 [7] Biostrings_2.73.1               XVector_0.45.0                 
 [9] shiny_1.9.1                     iSEEbug_0.1.0                  
[11] iSEE_2.17.3                     SingleCellExperiment_1.27.2    
[13] SummarizedExperiment_1.35.1     Biobase_2.65.0                 
[15] GenomicRanges_1.57.1            GenomeInfoDb_1.41.1            
[17] IRanges_2.39.2                  S4Vectors_0.43.2               
[19] BiocGenerics_0.51.0             MatrixGenerics_1.17.0          
[21] matrixStats_1.3.0              

loaded via a namespace (and not attached):
  [1] fs_1.6.4                    DirichletMultinomial_1.47.0
  [3] fontawesome_0.5.2           devtools_2.4.5             
  [5] httr_1.4.7                  RColorBrewer_1.1-3         
  [7] doParallel_1.0.17           profvis_0.3.8              
  [9] tools_4.4.0                 backports_1.5.0            
 [11] utf8_1.2.4                  R6_2.5.1                   
 [13] DT_0.33                     vegan_2.6-6.1              
 [15] lazyeval_0.2.2              mgcv_1.9-1                 
 [17] rhdf5filters_1.17.0         GetoptLong_1.0.5           
 [19] permute_0.9-7               urlchecker_1.0.1           
 [21] withr_3.0.1                 gridExtra_2.3              
 [23] cli_3.6.3                   textshaping_0.4.0          
 [25] Cairo_1.6-2                 shinyjs_2.1.0              
 [27] sandwich_3.1-0              labeling_0.4.3             
 [29] slam_0.1-51                 sass_0.4.9                 
 [31] mvtnorm_1.2-5               systemfonts_1.1.0          
 [33] yulab.utils_0.1.5           foreign_0.8-87             
 [35] scater_1.33.4               decontam_1.25.0            
 [37] sessioninfo_1.2.2           rstudioapi_0.16.0          
 [39] generics_0.1.3              gridGraphics_0.5-1         
 [41] shape_1.4.6.1               crosstalk_1.2.1            
 [43] dplyr_1.1.4                 rbiom_1.0.3                
 [45] Matrix_1.7-0                biomformat_1.33.0          
 [47] ggbeeswarm_0.7.2            fansi_1.0.6                
 [49] DECIPHER_3.1.4              abind_1.4-5                
 [51] lifecycle_1.0.4             yaml_2.3.10                
 [53] rhdf5_2.49.0                SparseArray_1.5.26         
 [55] grid_4.4.0                  promises_1.3.0             
 [57] crayon_1.5.3                shinydashboard_0.7.2       
 [59] miniUI_0.1.1.1              lattice_0.22-6             
 [61] beachmat_2.21.5             pillar_1.9.0               
 [63] knitr_1.48                  ComplexHeatmap_2.21.0      
 [65] rjson_0.2.21                boot_1.3-30                
 [67] lpSolve_5.6.20              codetools_0.2-20           
 [69] glue_1.7.0                  ggfun_0.1.5                
 [71] data.table_1.15.4           remotes_2.5.0              
 [73] vctrs_0.6.5                 png_0.1-8                  
 [75] treeio_1.29.0               gtable_0.3.5               
 [77] cachem_1.1.0                xfun_0.46                  
 [79] S4Arrays_1.5.5              mime_0.12                  
 [81] tidygraph_1.3.1             rsconnect_1.3.1            
 [83] iterators_1.0.14            bluster_1.15.0             
 [85] ellipsis_0.3.2              nlme_3.1-165               
 [87] ggtree_3.13.0               usethis_2.2.3              
 [89] rprojroot_2.0.4             bslib_0.8.0                
 [91] irlba_2.3.5.1               vipor_0.4.7                
 [93] rpart_4.1.23                colorspace_2.1-1           
 [95] DBI_1.2.3                   Hmisc_5.1-3                
 [97] nnet_7.3-19                 tidyselect_1.2.1           
 [99] compiler_4.4.0              htmlTable_2.4.3            
[101] BiocNeighbors_1.23.0        desc_1.4.3                 
[103] DelayedArray_0.31.9         colourpicker_1.3.0         
[105] checkmate_2.3.1             scales_1.3.0               
[107] stringr_1.5.1               digest_0.6.36              
[109] minqa_1.2.7                 rmarkdown_2.27             
[111] htmltools_0.5.8.1           pkgconfig_2.0.3            
[113] iSEEtree_0.99.5             base64enc_0.1-3            
[115] lme4_1.1-35.5               sparseMatrixStats_1.17.2   
[117] listviewer_4.0.0            fastmap_1.2.0              
[119] rlang_1.1.4                 GlobalOptions_0.1.2        
[121] htmlwidgets_1.6.4           UCSC.utils_1.1.0           
[123] DelayedMatrixStats_1.27.2   farver_2.1.2               
[125] jquerylib_0.1.4             zoo_1.8-12                 
[127] jsonlite_1.8.8              BiocParallel_1.39.0        
[129] BiocSingular_1.21.2         magrittr_2.0.3             
[131] Formula_1.2-5               scuttle_1.15.0             
[133] GenomeInfoDbData_1.2.12     ggplotify_0.1.2            
[135] patchwork_1.2.0             Rhdf5lib_1.27.0            
[137] munsell_0.5.1               Rcpp_1.0.13                
[139] ape_5.8                     ggnewscale_0.5.0           
[141] viridis_0.6.5               stringi_1.8.4              
[143] rintrojs_0.3.4              zlibbioc_1.51.1            
[145] MASS_7.3-61                 plyr_1.8.9                 
[147] mediation_4.5.0             pkgbuild_1.4.4             
[149] parallel_4.4.0              ggrepel_0.9.5              
[151] graphlayouts_1.1.1          splines_4.4.0              
[153] circlize_0.4.16             igraph_2.0.3               
[155] reshape2_1.4.4              ScaledMatrix_1.13.0        
[157] pkgload_1.4.0               evaluate_0.24.0            
[159] RcppParallel_5.1.8          nloptr_2.1.1               
[161] foreach_1.5.2               tweenr_2.0.3               
[163] httpuv_1.6.15               tidyr_1.3.1                
[165] purrr_1.0.2                 polyclip_1.10-7            
[167] clue_0.3-65                 ggforce_0.4.2              
[169] rsvd_1.0.5                  xtable_1.8-4               
[171] tidytree_0.4.6              later_1.3.2                
[173] viridisLite_0.4.2           ragg_1.3.2                 
[175] tibble_3.2.1                aplot_0.2.3                
[177] memoise_2.0.1               beeswarm_0.4.0             
[179] cluster_2.1.6               shinyWidgets_0.8.6         
[181] shinyAce_0.4.2
TuomasBorman commented 3 months ago

Hi! Thanks, this is related to renaming parameters, and there was a single typo