mixOmics 3D scatterplot for individuals not displaying
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Entering edit mode
Blobby123 • 0
@6e53f140
Last seen 5 months ago
United Kingdom

The plotIndiv function works with the lattice style on my data but doesn't display a plot when the style is changed to "3d". Please could you help me fix this.

pca <- pca(RESP, ncomp = 6, scale = TRUE)

x11()
plotIndiv(pca, ind.names=Samples, 
          group=as.numeric(as.factor(class)), 
          style="3d")

sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] rgl_0.108.3       mixOmics_6.18.1   ggplot2_3.3.5     lattice_0.20-45   MASS_7.3-54      
[6] R.matlab_3.6.2    plsgenomics_1.5-2 matlab_1.0.2     

loaded via a namespace (and not attached):
 [1] spam_2.7-0             xfun_0.28              tidyselect_1.1.1       reshape2_1.4.4        
 [5] purrr_0.3.4            colorspace_2.0-2       vctrs_0.3.8            generics_0.1.1        
 [9] htmltools_0.5.2        viridisLite_0.4.0      utf8_1.2.2             rlang_0.4.12          
[13] R.oo_1.24.0            pillar_1.6.4           glue_1.5.1             withr_2.4.3           
[17] R.utils_2.11.0         BiocParallel_1.28.2    RColorBrewer_1.1-2     matrixStats_0.61.0    
[21] lifecycle_1.0.1        plyr_1.8.6             stringr_1.4.0          fields_13.3           
[25] dotCall64_1.0-1        munsell_0.5.0          gtable_0.3.0           R.methodsS3_1.8.1     
[29] htmlwidgets_1.5.4      knitr_1.36             fastmap_1.1.0          parallel_4.1.2        
[33] fansi_0.5.0            rARPACK_0.11-0         Rcpp_1.0.7             corpcor_1.6.10        
[37] scales_1.1.1           BiocManager_1.30.16    jsonlite_1.7.2         RSpectra_0.16-0       
[41] gridExtra_2.3          ellipse_0.4.2          RhpcBLASctl_0.21-247.1 digest_0.6.29         
[45] stringi_1.7.6          dplyr_1.0.7            ggrepel_0.9.1          grid_4.1.2            
[49] tools_4.1.2            magrittr_2.0.1         maps_3.4.0             tibble_3.1.6          
[53] crayon_1.4.2           tidyr_1.1.4            pkgconfig_2.0.3        ellipsis_0.3.2        
[57] Matrix_1.4-0           viridis_0.6.2          R6_2.5.1               boot_1.3-28           
[61] igraph_1.2.9           compiler_4.1.2
plotIndiv 3D mixOmics PCA • 247 views
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1
Entering edit mode
Blobby123 • 0
@6e53f140
Last seen 5 months ago
United Kingdom

I fixed the issue by reinstalling rgl and mixOmics libraries.

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