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
Just checked and increasing replicate number to 3 allows plotting of means. I am assuming this is some hard coded limitation of ballgown. If anyone else is finding this and could comment just to confirm that would be appreciated.