faceting MAplots?

[eterlova]

Hello, I want to make a panel with multiple MA plots for my RNAseq data, but for some reason facet() function does not recognize the column names?

I have a data frame, which was composed from multiple ones containing log2foldchange information for RNA seq of several species and different conditions measured:

> str(MA_data)
'data.frame':	518949 obs. of  8 variables:
 $ baseMean      : num  4082.9 454 483.6 11.6 23457.9 ...
 $ log2FoldChange: num  5.00e-07 -3.20e-07 6.14e-08 3.41e-07 1.02e-06 ...
 $ lfcSE         : num  0.00144 0.00144 0.00144 0.00144 0.00144 ...
 $ pvalue        : num  0.986 0.682 0.981 0.528 0.141 ...
 $ padj          : num  0.998 0.978 0.997 0.955 0.8 ...
 $ gene          : chr  "DN0c0g1" "DN0c0g2" "DN0c0g4" "DN0c12g1" ...
 $ Condition     : chr  "Desiccated vs Hydrated" "Desiccated vs Hydrated" "Desiccated vs Hydrated" "Desiccated vs Hydrated" ...
 $ species       : chr  "ZA17" "ZA17" "ZA17" "ZA17" ...

Then I go ahead to make a "frankenstein" plot (this works) to be split later:

ma <- ggmaplot(MA_data, fdr = 0.1, fc = 2, size = 0.4,
         palette = c("#B31B21", "#1465AC", "darkgray"),
         legend = "top", top = 20,
         font.label = c("bold", 11),
         font.legend = "bold",
         font.main = "bold")

But when I use facet(), there is an error:

facet(ma, facet.by = "species")
Error in `combine_vars()`:
! At least one layer must contain all faceting variables: `species`.
* Plot is missing `species`
* Layer 1 is missing `species`
* Layer 2 is missing `species`
* Layer 3 is missing `species`

I thought to facet the plot, the columns need to be present in the data rather than the plot? what am I doing wrong?

Best, Lisa

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.0.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] gridExtra_2.3               tidyr_1.2.1                 ggpubr_0.4.0               
 [4] DESeq2_1.34.0               SummarizedExperiment_1.24.0 MatrixGenerics_1.6.0       
 [7] matrixStats_0.62.0          GenomicRanges_1.46.1        GenomeInfoDb_1.30.1        
[10] IRanges_2.28.0              S4Vectors_0.32.4            dplyr_1.0.10               
[13] ggplot2_3.3.6               genefilter_1.76.0           qvalue_2.26.0              
[16] Biobase_2.54.0              BiocGenerics_0.40.0         cluster_2.1.4              

loaded via a namespace (and not attached):
 [1] httr_1.4.4             bit64_4.0.5            splines_4.1.2          carData_3.0-5         
 [5] assertthat_0.2.1       blob_1.2.3             GenomeInfoDbData_1.2.7 ggrepel_0.9.1         
 [9] pillar_1.8.1           RSQLite_2.2.17         backports_1.4.1        lattice_0.20-45       
[13] glue_1.6.2             digest_0.6.29          RColorBrewer_1.1-3     XVector_0.34.0        
[17] ggsignif_0.6.3         colorspace_2.0-3       Matrix_1.5-1           plyr_1.8.7            
[21] XML_3.99-0.10          pkgconfig_2.0.3        broom_1.0.1            zlibbioc_1.40.0       
[25] purrr_0.3.4            xtable_1.8-4           scales_1.2.1           BiocParallel_1.28.3   
[29] tibble_3.1.8           annotate_1.72.0        KEGGREST_1.34.0        farver_2.1.1          
[33] generics_0.1.3         car_3.1-0              ellipsis_0.3.2         cachem_1.0.6          
[37] withr_2.5.0            cli_3.4.1              survival_3.4-0         magrittr_2.0.3        
[41] crayon_1.5.2           memoise_2.0.1          fansi_1.0.3            rstatix_0.7.0         
[45] tools_4.1.2            lifecycle_1.0.1        stringr_1.4.1          munsell_0.5.0         
[49] locfit_1.5-9.6         ggsci_2.9              DelayedArray_0.20.0    AnnotationDbi_1.56.2  
[53] Biostrings_2.62.0      compiler_4.1.2         rlang_1.0.6            grid_4.1.2            
[57] RCurl_1.98-1.8         rstudioapi_0.14        labeling_0.4.2         bitops_1.0-7          
[61] gtable_0.3.1           abind_1.4-5            DBI_1.1.3              reshape2_1.4.4        
[65] R6_2.5.1               fastmap_1.1.0          bit_4.0.4              utf8_1.2.2            
[69] stringi_1.7.8          parallel_4.1.2         Rcpp_1.0.9             vctrs_0.4.1           
[73] geneplotter_1.72.0     png_0.1-7              tidyselect_1.1.2