I am trying to use the ballgown Plotmeans function to display side-by-side plots of transcript level expression under 3 different experimental conditions (3 conditions with only 2 replicates per condition).

I am using the following code:

plotMeans("MSTRG.8",bg_data_filt,groupvar = "Condition", groupname = "all",  meas = "FPKM", colorby = "transcript")

but only getting 1 plot (the first displayed) in R-Studio. No error message is shown.

I have used the plotTranscripts function and that seems to display my 6 samples side-by-side with no problem:

plotTranscripts(gene = 'MSTRG.8',bg_data_filt, samples=c("1a","1b","2a","2b","3a","3b"), meas = 'FPKM', colorby = 'transcript', labelTranscripts = TRUE)

Can anybody offer any suggestions as to why plotMeans isn't working as intended?

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               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] ballgown_2.10.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17               compiler_3.4.4             RColorBrewer_1.1-2         GenomeInfoDb_1.14.0       
 [5] XVector_0.18.0             bitops_1.0-6               tools_3.4.4                zlibbioc_1.24.0           
 [9] digest_0.6.15              bit_1.1-14                 nlme_3.1-137               annotate_1.56.2           
[13] RSQLite_2.1.1              memoise_1.1.0              lattice_0.20-35            mgcv_1.8-24               
[17] Matrix_1.2-14              DelayedArray_0.4.1         DBI_1.0.0                  parallel_3.4.4            
[21] GenomeInfoDbData_1.0.0     rtracklayer_1.38.3         genefilter_1.60.0          Biostrings_2.46.0         
[25] S4Vectors_0.16.0           IRanges_2.12.0             stats4_3.4.4               bit64_0.9-7               
[29] grid_3.4.4                 Biobase_2.38.0             AnnotationDbi_1.40.0       XML_3.98-1.11             
[33] survival_2.42-6            BiocParallel_1.12.0        limma_3.34.9               sva_3.26.0                
[37] blob_1.1.1                 Rsamtools_1.30.0           matrixStats_0.53.1         GenomicAlignments_1.14.2  
[41] splines_3.4.4              BiocGenerics_0.24.0        GenomicRanges_1.30.3       SummarizedExperiment_1.8.1
[45] xtable_1.8-2               RCurl_1.95-4.10