Error: In has.phylogeny(), biom must be a BIOM-class objec
Closed this issue · 8 comments
nick-youngblut commented
Reprex
library(rbiom)
# Using a custom matrix and tree
mtx <- matrix(sample.int(12*20), ncol=20)
dimnames(mtx) <- list(LETTERS[1:12], letters[1:20])
tree <- ape::as.phylo(hclust(dist(mtx)))
dm <- unifrac(mtx, tree=tree)
dm
Error
Error: In has.phylogeny(), biom must be a BIOM-class object.
Traceback:
1. unifrac(mtx, tree = tree)
2. rbiom::beta.div(biom, "unifrac", weighted, tree)
3. validate_metrics(biom, method, mode = "bdiv")
4. do.call(paste0(mode, "_metrics"), list(biom = biom))
5. bdiv_metrics(biom = structure(c(123L, 63L, 209L, 179L, 159L,
. 232L, 99L, 205L, 74L, 104L, 208L, 161L, 3L, 80L, 139L, 214L,
. 203L, 169L, 12L, 96L, 225L, 46L, 39L, 76L, 220L, 207L, 10L, 212L,
. 109L, 106L, 165L, 81L, 83L, 158L, 184L, 86L, 93L, 235L, 134L,
. 150L, 71L, 239L, 62L, 28L, 198L, 167L, 23L, 113L, 58L, 5L, 128L,
. 15L, 25L, 147L, 57L, 172L, 133L, 42L, 35L, 199L, 97L, 77L, 143L,
. 230L, 121L, 127L, 69L, 51L, 20L, 38L, 122L, 101L, 114L, 141L,
. 36L, 27L, 157L, 49L, 138L, 6L, 217L, 84L, 70L, 4L, 200L, 52L,
. 89L, 181L, 65L, 18L, 130L, 8L, 228L, 17L, 146L, 61L, 131L, 31L,
. 118L, 152L, 140L, 176L, 40L, 45L, 221L, 189L, 19L, 87L, 237L,
. 66L, 82L, 129L, 68L, 91L, 22L, 185L, 142L, 44L, 180L, 136L, 233L,
. 219L, 168L, 126L, 125L, 119L, 191L, 210L, 116L, 144L, 154L, 148L,
. 196L, 33L, 21L, 224L, 234L, 223L, 202L, 153L, 226L, 190L, 100L,
. 43L, 14L, 1L, 156L, 215L, 137L, 111L, 90L, 177L, 41L, 92L, 238L,
. 112L, 193L, 187L, 240L, 135L, 47L, 2L, 201L, 115L, 213L, 37L,
. 7L, 26L, 54L, 149L, 151L, 183L, 182L, 103L, 72L, 195L, 155L,
. 236L, 48L, 164L, 59L, 9L, 188L, 218L, 55L, 75L, 163L, 30L, 231L,
. 60L, 171L, 78L, 132L, 211L, 194L, 162L, 98L, 56L, 173L, 192L,
. 16L, 216L, 110L, 53L, 102L, 175L, 50L, 11L, 206L, 124L, 222L,
. 13L, 34L, 120L, 229L, 79L, 117L, 178L, 186L, 73L, 166L, 108L,
. 227L, 197L, 67L, 94L, 29L, 174L, 24L, 170L, 145L, 85L, 160L,
. 204L, 64L, 88L, 105L, 95L, 107L, 32L), .Dim = c(12L, 20L), .Dimnames = list(
. c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K",
. "L"), c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j",
. "k", "l", "m", "n", "o", "p", "q", "r", "s", "t"))))
6. metrics(biom, "bdiv")
7. has.phylogeny(biom)
sessionInfo
R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS
Matrix products: default
BLAS/LAPACK: /ebio/abt3_projects/Georg_animal_feces/envs/phyloseq2a/lib/libopenblasp-r0.3.17.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rbiom_1.0.2.9038 LeyLabRMisc_0.2.0 vegan_2.5-7 lattice_0.20-44
[5] permute_0.9-5 phyloseq_1.36.0 ape_5.5 tidytable_0.6.5
[9] data.table_1.14.0 ggplot2_3.3.5 tidyr_1.1.3 dplyr_1.0.7
loaded via a namespace (and not attached):
[1] Biobase_2.52.0 jsonlite_1.7.2 splines_4.1.1
[4] foreach_1.5.1 RcppParallel_5.1.4 stats4_4.1.1
[7] GenomeInfoDbData_1.2.6 slam_0.1-48 ggrepel_0.9.1
[10] pillar_1.6.2 glue_1.4.2 uuid_0.1-4
[13] digest_0.6.27 XVector_0.32.0 stringfish_0.15.2
[16] colorspace_2.0-2 htmltools_0.5.2 Matrix_1.3-4
[19] plyr_1.8.6 pkgconfig_2.0.3 zlibbioc_1.38.0
[22] purrr_0.3.4 scales_1.1.1 RApiSerialize_0.1.0
[25] tibble_3.1.4 mgcv_1.8-36 generics_0.1.0
[28] IRanges_2.26.0 ellipsis_0.3.2 withr_2.4.2
[31] repr_1.1.3 BiocGenerics_0.38.0 survival_3.2-13
[34] magrittr_2.0.1 crayon_1.4.1 evaluate_0.14
[37] fansi_0.4.2 doParallel_1.0.16 nlme_3.1-153
[40] MASS_7.3-54 tools_4.1.1 lifecycle_1.0.0
[43] stringr_1.4.0 Rhdf5lib_1.14.0 S4Vectors_0.30.0
[46] munsell_0.5.0 cluster_2.1.2 Biostrings_2.60.0
[49] ade4_1.7-17 compiler_4.1.1 GenomeInfoDb_1.28.0
[52] qs_0.25.1 rlang_0.4.11 rhdf5_2.36.0
[55] grid_4.1.1 RCurl_1.98-1.5 pbdZMQ_0.3-5
[58] iterators_1.0.13 IRkernel_1.2 rhdf5filters_1.4.0
[61] biomformat_1.20.0 igraph_1.2.6 bitops_1.0-7
[64] base64enc_0.1-3 gtable_0.3.0 codetools_0.2-18
[67] multtest_2.48.0 reshape2_1.4.4 R6_2.5.1
[70] fastmap_1.1.0 utf8_1.2.2 stringi_1.7.4
[73] parallel_4.1.1 IRdisplay_1.0 Rcpp_1.0.7
[76] vctrs_0.3.8 tidyselect_1.1.1
nick-youngblut commented
This does not produce an error:
biom <- select(hmp50, 1:10)
dm <- unifrac(biom)
nick-youngblut commented
The error seems to be due to:
metrics <- function (biom, mode) {
mode <- tolower(mode)[[1]]
if (!is(biom, 'BIOM') && mode %in% c('rank', 'taxon', 'meta'))
stop("Please provide a BIOM object when using mode='", mode, "'")
if (mode == 'ord') { c("PCoA", "tSNE", "NMDS")
} else if (mode == 'adiv') { c("OTUs", "Shannon", "Chao1", "Simpson", "InvSimpson")
} else if (mode == 'dist') { c("correlation", "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski")
} else if (mode == 'clust') { c("average", "ward", "mcquitty", "single", "median", "complete", "centroid")
} else if (mode == 'rank') { taxa.ranks(biom)
} else if (mode == 'taxon') { unique(c(as.character(taxonomy(biom)), taxa.names(biom)))
} else if (mode == 'meta') { colnames(metadata(biom))
} else if (mode == 'bdiv') {
if (has.phylogeny(biom)) { c("Manhattan", "Euclidean", "Bray-Curtis", "Jaccard", "UniFrac")
} else { c("Manhattan", "Euclidean", "Bray-Curtis", "Jaccard") }
} else { NULL }
}
...where you are assuming the biom object is actually a biom-class object. Maybe !is(biom, 'BIOM') && mode %in% c('rank', 'taxon', 'meta') isn't actually checking for biom class due to && mode %in% c('rank', 'taxon', 'meta')?
dansmith01 commented
Thanks for the heads up and investigation on this, @nick-youngblut. Fixed!
nick-youngblut commented
Thanks for the quick fix!
FYI: I'm planning on creating a conda-forge recipe for rbiom, unless you are planning on creating one in the near future.
dansmith01 commented
That's a great idea! I didn't realize until just now that conda handles r packages too. I'm pushing CRAN's version of rbiom over there now and will update this thread when it's in place.
The next couple weeks should see the current development branch submitted to CRAN, and I'll update conda-forge then as well.
nick-youngblut commented
Great! Yeah, conda (especially with mamba) can be a one-stop-shop for installing all bioinformatics software than one generally needs, including R packages and other non-python software. I highly recommend it.
I'm looking forward to seeing rbiom on conda-forge!
dansmith01 commented
@nick-youngblut Now on conda-forge!
https://anaconda.org/conda-forge/r-rbiom
nick-youngblut commented
Awesome!! 🎉
Thanks for adding rbiom to conda-forge!