Hi Elizabeth,

Thanks for the report. Apparently, it's enough to add:

    if (is.null(p)) p <- 1L


    p <- ncol(x)

Best wishes,


Le 23/05/2017 à 20:31, Elizabeth Purdom a écrit :

I am writing to the R-sig-phylo mailing list regarding what seems to be a bug in the `phydataplot` function in `ape`.

Specifically, if the style is `mosaic` but the data is a vector or 1-column matrix, the function fails.

The following code is from the examples (that obviously works):
 > tr <- rtree(n <- 30)
 > p <- 5
 > x <- matrix(sample(3, size = n*p, replace = TRUE), n, p)
 > dimnames(x) <- list(paste0("t", 1:n), LETTERS[1:p])
 > plot(tr, x.lim = 35, align.tip = TRUE, adj = 1)
 > phydataplot(x, tr, "m", 2)

However, if I instead use only 1 column of x (either vector or force to remain a matrix):

 > phydataplot(x[,1],tr,"m",2)
Error in seq.default(x0, x1, width) : invalid (to - from)/by in seq(.)
 > phydataplot(x[,1,drop=FALSE],tr,"m",2)
Error in seq.default(x0, x1, width) : invalid (to - from)/by in seq(.)

This appears to be because of the following code within the function:
p <- ncol(x)
if (is.null(width)) {
             x1 <- lastPP$x.lim[2]
             width <- (x1 - x0)/p
} else x1 <- x0 + width * p
xx <- seq(x0, x1, width)

Since `x` is the output of `.matchDataPhylo(x, phy)`, it is always a vector, even if original x is a 1-column matrix, so that ncol(x) is NULL. Probably if there is a catch for when x is a vector to set p=1, then it would fix the problem, though I haven’t tested whether there are any further problems that come up.

All of the best,
Elizabeth Purdom

Here is my session info:
 > sessionInfo()
R version 3.3.0 beta (2016-04-04 r70420)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

[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] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] clusterExperiment_1.3.1 ape_4.1 SummarizedExperiment_1.4.0 [4] Biobase_2.34.0 GenomicRanges_1.26.4 GenomeInfoDb_1.10.3 [7] IRanges_2.8.2 S4Vectors_0.12.2 BiocGenerics_0.20.0
[10] devtools_1.12.0

loaded via a namespace (and not attached):
[1] nlme_3.1-131 bitops_1.0-6 matrixStats_0.52.2 bold_0.4.0 doParallel_1.0.10 [6] RColorBrewer_1.1-2 progress_1.1.2 httr_1.2.1 prabclus_2.2-6 tools_3.3.0 [11] R6_2.2.0 DBI_0.6-1 lazyeval_0.2.0 colorspace_1.3-2 ade4_1.7-6 [16] trimcluster_0.1-2 nnet_7.3-12 withr_1.0.2 gridExtra_2.2.1 prettyunits_1.0.2 [21] xml2_1.1.1 pkgmaker_0.22 diptest_0.75-7 scales_0.4.1 DEoptimR_1.0-8 [26] mvtnorm_1.0-6 robustbase_0.92-7 NMF_0.20.6 commonmark_1.2 stringr_1.2.0 [31] digest_0.6.12 XVector_0.14.1 limma_3.30.13 howmany_0.3-1 jsonlite_1.4 [36] mclust_5.2.3 dendextend_1.5.2 dplyr_0.5.0 RCurl_1.95-4.8 magrittr_1.5 [41] modeltools_0.2-21 Matrix_1.2-10 Rcpp_0.12.10 munsell_0.4.3 abind_1.4-5 [46] viridis_0.4.0 stringi_1.1.5 whisker_0.3-2 MASS_7.3-47 zlibbioc_1.20.0 [51] flexmix_2.3-14 MAST_1.0.5 plyr_1.8.4 grid_3.3.0 crayon_1.3.2 [56] rncl_0.8.2 lattice_0.20-35 splines_3.3.0 uuid_0.1-2 taxize_0.8.4 [61] fpc_2.1-10 rngtools_1.2.4 reshape2_1.4.2 codetools_0.2-15 XML_3.98-1.7 [66] RNeXML_2.0.7 data.table_1.10.4 foreach_1.4.3 testthat_1.0.2 locfdr_1.1-8 [71] gtable_0.2.0 tidyr_0.6.2 reshape_0.8.6 kernlab_0.9-25 assertthat_0.2.0 [76] ggplot2_2.2.1 gridBase_0.4-7 phylobase_0.8.4 xtable_1.8-2 roxygen2_6.0.1 [81] class_7.3-14 viridisLite_0.2.0 tibble_1.3.0 iterators_1.0.8 registry_0.3
[86] memoise_1.1.0      cluster_2.0.6

Pour nous remonter une erreur de filtrage, veuillez vous rendre ici <http://f.security-mail.net/803CxvOn8RA>

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