indY cannot be used in block.spls for circosPlot()

[Max-Bladen]

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🐞 Describe the bug:

The only way that circosPlot() can be used on a block.spls object is if the Y dataframe is supplied separately. Essentially makes the indY parameter redundant in this context.

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🔍 reprex results from reproducible example including sessioninfo():

### --- SET UP DATA --- ###

suppressMessages(library(mixOmics)) # load package and data
data(breast.TCGA)

## class membership
breast.group = breast.TCGA$data.train$subtype

## data1 has all dataframes
breast.data1 <- list(mirna = breast.TCGA$data.train$mirna,
                    mrna = breast.TCGA$data.train$mrna,
                    protein = breast.TCGA$data.train$protein)

## data2 has all but protein data
breast.data2 <- list(mirna = breast.TCGA$data.train$mirna,
                    mrna = breast.TCGA$data.train$mrna)

### --- RUN BLOCK.SPLS --- ###

## form block.spls with combined dataframes
breast.block.spls.comb <- block.spls(breast.data1, indY = 3,
                                     keepX = list(mirna = c(10,10),
                                                  mrna = c(10,10)))

## form block.spls with separated dataframes
breast.block.spls.sep <- block.spls(breast.data2, breast.TCGA$data.train$protein,
                                    keepX = list(mirna = c(10,10),
                                                 mrna = c(10,10)))

### --- PASS TO CIRCOS.PLOT --- ###

## works, can find object$X$Y
circosPlot(breast.block.spls.sep, group = breast.group, 
           cutoff = 0.8) 

## ERROR RAISED !
circosPlot(breast.block.spls.comb, group = breast.group, 
           cutoff = 0.8)
#> Error in if (length(group) != nrow(object$X$Y)) stop("group must be a factor of length: nrow(object$X$Y) = ", : argument is of length zero

^{Created on 2022-03-08 by the reprex package (v2.0.1)}

Session info

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     2022-03-08
#>  pandoc   2.14.2 @ C:/Users/Work/AppData/Local/Pandoc/ (via rmarkdown)
#> 
#> - Packages -------------------------------------------------------------------
#>  package      * version date (UTC) lib source
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#>  BiocParallel   1.28.1  2021-11-18 [1] Bioconductor
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#> 
#> ------------------------------------------------------------------------------

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🤔 Expected behavior:

Seeing as within block.spls(), both setting Y explicitly or using the indY parameter are both valid, having the circosPlot() only function in one of these scenarios is suboptimal.

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💡 Possible solution:

Seeing as error raised claims that nrow(object$X$Y) is of length 0, this means that the $X$Y component is likely not set when indY is used.