cim() function cannot take pca objects

[Max-Bladen]

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🐞 Describe the bug: Passing a pca object to the cim() function will yield the follow error:

Error in abs(mat$rotation) : non-numeric argument to mathematical function

This only occurs with pca (not spca, sipca or ipca) objects. No change results from adjusting the cim() input parameters from their defaults.

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🔍 reprex results from reproducible example including sessioninfo():

library(mixOmics)
data(liver.toxicity)
liver.pca <- pca(liver.toxicity$gene, ncomp=2) 
cim(liver.pca) 
#> Error in abs(mat$rotation): non-numeric argument to mathematical function

^{Created on 2022-03-07 by the reprex package (v2.0.1)}

Session info

``` r sessioninfo::session_info() #> - Session info --------------------------------------------------------------- #> setting value #> version R version 4.1.2 Patched (2021-11-16 r81220) #> os Windows 10 x64 (build 19042) #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate English_Australia.1252 #> ctype English_Australia.1252 #> tz Australia/Sydney #> date 2022-03-07 #> pandoc 2.14.2 @ C:/Users/Work/AppData/Local/Pandoc/ (via rmarkdown) #> #> - Packages ------------------------------------------------------------------- #> package * version date (UTC) lib source #> backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.2) #> BiocParallel 1.28.1 2021-11-18 [1] Bioconductor #> cli 3.2.0 2022-02-14 [1] CRAN (R 4.1.2) #> colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.1.2) #> corpcor 1.6.10 2021-09-16 [1] CRAN (R 4.1.1) #> crayon 1.5.0 2022-02-14 [1] CRAN (R 4.1.2) #> digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.2) #> dplyr 1.0.8 2022-02-08 [1] CRAN (R 4.1.2) #> ellipse 0.4.2 2020-05-27 [1] CRAN (R 4.1.2) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.2) #> evaluate 0.15 2022-02-18 [1] CRAN (R 4.1.2) #> fansi 1.0.2 2022-01-14 [1] CRAN (R 4.1.2) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.2) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.2) #> generics 0.1.2 2022-01-31 [1] CRAN (R 4.1.2) #> ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.1.2) #> ggrepel 0.9.1 2021-01-15 [1] CRAN (R 4.1.2) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2) #> gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.2) #> gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.2) #> highr 0.9 2021-04-16 [1] CRAN (R 4.1.2) #> htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.2) #> igraph 1.2.11 2022-01-04 [1] CRAN (R 4.1.2) #> knitr 1.37 2021-12-16 [1] CRAN (R 4.1.2) #> lattice * 0.20-45 2021-09-22 [2] CRAN (R 4.1.2) #> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.2) #> magrittr 2.0.2 2022-01-26 [1] CRAN (R 4.1.2) #> MASS * 7.3-54 2021-05-03 [2] CRAN (R 4.1.2) #> Matrix 1.3-4 2021-06-01 [2] CRAN (R 4.1.2) #> matrixStats 0.61.0 2021-09-17 [1] CRAN (R 4.1.2) #> mixOmics * 6.18.1 2021-11-18 [1] Bioconductor (R 4.1.2) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.2) #> pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.2) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.2) #> plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.2) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.2) #> R.cache 0.15.0 2021-04-30 [1] CRAN (R 4.1.2) #> R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.1.1) #> R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.1.1) #> R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.1.2) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.2) #> rARPACK 0.11-0 2016-03-10 [1] CRAN (R 4.1.2) #> RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.1) #> Rcpp 1.0.8 2022-01-13 [1] CRAN (R 4.1.2) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.2) #> reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.2) #> rlang 1.0.1 2022-02-03 [1] CRAN (R 4.1.2) #> rmarkdown 2.12 2022-03-02 [1] CRAN (R 4.1.2) #> RSpectra 0.16-0 2019-12-01 [1] CRAN (R 4.1.2) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.2) #> scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.2) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2) #> stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.2) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.2) #> styler 1.6.2 2021-09-23 [1] CRAN (R 4.1.2) #> tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.2) #> tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.1.2) #> tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.1.2) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.2) #> vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.2) #> withr 2.4.3 2021-11-30 [1] CRAN (R 4.1.2) #> xfun 0.30 2022-03-02 [1] CRAN (R 4.1.2) #> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.1.2) #> #> [1] C:/Users/Work/Documents/R/win-library/4.1 #> [2] C:/Program Files/R/R-4.1.2patched/library #> #> ------------------------------------------------------------------------------ ```

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🤔 Expected behavior: In the way that cim() functions properly on a spca object, yielding a heatmap of the variate values, cim() on a pca object should yield the same.

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💡 Possible solution: The issue seems to be caused by inconsistencies between the output of the pca() and spca() function. Within cim(), these object types are handled via the same code but have differing output components. pca does not contain the $x or $rotation components. Hence, rectifying this heterogeneity may solve the issue

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Upon Completion: Adjust "Common Errors" page on mixOmics.org