mixOmics 3D scatterplot for individuals not displaying
1
0
Entering edit mode
Blobby123 • 0
@6e53f140
Last seen 18 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 • 1.1k views
ADD COMMENT
1
Entering edit mode
Blobby123 • 0
@6e53f140
Last seen 18 months ago
United Kingdom

I fixed the issue by reinstalling rgl and mixOmics libraries.

ADD COMMENT

Login before adding your answer.

Traffic: 698 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6