Hi,
I was trying out the phyloseq example at http://joey711.github.io/phyloseq/import-data
Here is my code and the error I get:
================
> OTU = otu_table(otumat, taxa_are_rows = TRUE)
> TAX = tax_table(taxmat)
>
> physeq = phyloseq(OTU, TAX)
> physeq
phyloseq-class experiment-level object
otu_table() OTU Table: [ 10 taxa and 10 samples ]
tax_table() Taxonomy Table: [ 10 taxa by 7 taxonomic ranks ]
>
> plot_bar(physeq, fill = "Family")
Error in .Method(..., na.last = na.last, decreasing = decreasing) :
argument 1 is not a vector
============
my session info:
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
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 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] ape_3.3 phyloseq_1.12.2
[3] MASS_7.3-44 edgeR_3.10.5
[5] permute_0.8-4 airway_0.102.0
[7] metagenomeSeq_1.10.0 limma_3.24.15
[9] lubridate_1.3.3 gridExtra_2.0.0
[11] scales_0.3.0 RColorBrewer_1.1-2
[13] hash_2.2.6 ggplot2_1.0.1
[15] FDb.InfiniumMethylation.hg19_2.2.0 org.Hs.eg.db_3.1.2
[17] RSQLite_1.0.0 DBI_0.3.1
[19] TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2 GenomicFeatures_1.20.6
[21] AnnotationDbi_1.30.1 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
[23] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.14.0
[25] bumphunter_1.8.0 locfit_1.5-9.1
[27] iterators_1.0.8 Biostrings_2.36.4
[29] XVector_0.8.0 GenomicRanges_1.20.8
[31] GenomeInfoDb_1.4.3 IRanges_2.2.9
[33] S4Vectors_0.6.6 lattice_0.20-33
[35] Biobase_2.28.0 BiocGenerics_0.14.0
[37] biomaRt_2.24.1 reshape_0.8.5
[39] foreach_1.4.3 foreign_0.8-66
[41] preprocessCore_1.30.0 BiocInstaller_1.18.5
[43] tsne_0.1-2
loaded via a namespace (and not attached):
[1] nlme_3.1-122 bitops_1.0-6 matrixStats_0.15.0 tools_3.2.0 doRNG_1.6
[6] nor1mix_1.2-1 vegan_2.3-1 rpart_4.1-10 KernSmooth_2.23-15 mgcv_1.8-7
[11] Hmisc_3.17-0 colorspace_1.2-6 nnet_7.3-11 ade4_1.7-2 DESeq2_1.8.2
[16] base64_1.1 chron_2.3-47 pkgmaker_0.22 rtracklayer_1.28.10 labeling_0.3
[21] caTools_1.17.1 genefilter_1.50.0 quadprog_1.5-5 stringr_1.0.0 digest_0.6.8
[26] Rsamtools_1.20.5 illuminaio_0.10.0 siggenes_1.42.0 GEOquery_2.34.0 mclust_5.1
[31] BiocParallel_1.2.22 gtools_3.5.0 acepack_1.3-3.3 RCurl_1.95-4.7 magrittr_1.5
[36] Formula_1.2-1 Matrix_1.2-2 futile.logger_1.4.1 Rcpp_0.12.1 munsell_0.4.2
[41] proto_0.3-10 stringi_1.0-1 RJSONIO_1.3-0 zlibbioc_1.14.0 gplots_2.17.0
[46] plyr_1.8.3 grid_3.2.0 gdata_2.17.0 splines_3.2.0 multtest_2.24.0
[51] annotate_1.46.1 beanplot_1.2 igraph_1.0.1 rngtools_1.2.4 geneplotter_1.46.0
[56] reshape2_1.4.1 codetools_0.2-14 futile.options_1.0.0 XML_3.98-1.3 RcppArmadillo_0.6.100.0.0
[61] latticeExtra_0.6-26 data.table_1.9.6 biom_0.3.12 lambda.r_1.1.7 gtable_0.1.2
[66] xtable_1.7-4 survival_2.38-3 GenomicAlignments_1.4.2 registry_0.3 memoise_0.2.1
[71] cluster_2.0.3
thanks!
