emilyvansyoc
commented
2 years ago Hi, not sure if you've already fixed this but it is working today :)
Closed emilyvansyoc closed 2 years ago
emilyvansyoc
commented
2 years ago Hi, not sure if you've already fixed this but it is working today :)
david-barnett
commented
2 years ago Hi Emily,
Thanks for the update, no I had not had time to look at it yet, so let me know if it happens again.
And I'm glad you've found microViz useful, your kind words mean a lot, thanks :)
Hello, Thanks for writing such a fantastic package. Gone are the days of manually extracting vegan objects and forcing them into ggplot!!
I'm following the heatmaps vignette and having this issue in v0.90. Is this a bug or user error (always more likely)?
Code:
psf %>%
glom to Order
tax_glom("Order") %>% tax_transform("compositional") %>% comp_heatmap(colors = heat_palette(palette = "Blue-Red"), sample_anno = sampleAnnotation( State1 = anno_sample("metformin"), col = list(State1 = cols), border = FALSE) )
sessionInfo:
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
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] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages: [1] RColorBrewer_1.1-2 ggvegan_0.1-0 ggpubr_0.4.0
[4] rstatix_0.7.0 dada2_1.20.0 Rcpp_1.0.8
[7] UpSetR_1.4.0 ComplexHeatmap_2.10.0 shiny_1.7.1
[10] microViz_0.9.0 phyloseq_1.38.0 forcats_0.5.1
[13] stringr_1.4.0 dplyr_1.0.8 purrr_0.3.4
[16] readr_2.1.2 tidyr_1.2.0 tibble_3.1.6
[19] ggplot2_3.3.5 tidyverse_1.3.1 vegan_2.5-7
[22] lattice_0.20-45 permute_0.9-7
loaded via a namespace (and not attached): [1] utf8_1.2.2 tidyselect_1.1.1
[3] htmlwidgets_1.5.4 TSP_1.1-11
[5] BiocParallel_1.26.2 Rtsne_0.15
[7] devtools_2.4.3 munsell_0.5.0
[9] codetools_0.2-18 DT_0.20
[11] withr_2.4.3 colorspace_2.0-2
[13] Biobase_2.54.0 rstudioapi_0.13
[15] stats4_4.1.2 ggsignif_0.6.3
[17] MatrixGenerics_1.4.3 labeling_0.4.2
[19] GenomeInfoDbData_1.2.7 hwriter_1.3.2
[21] farver_2.1.0 rhdf5_2.38.0
[23] rprojroot_2.0.2 vctrs_0.3.8
[25] generics_0.1.2 R6_2.5.1
[27] doParallel_1.0.17 GenomeInfoDb_1.30.1
[29] clue_0.3-60 seriation_1.3.1
[31] isoband_0.2.5 bitops_1.0-7
[33] rhdf5filters_1.6.0 microbiome_1.16.0
[35] cachem_1.0.6 DelayedArray_0.18.0
[37] assertthat_0.2.1 promises_1.2.0.1
[39] scales_1.1.1 gtable_0.3.0
[41] Cairo_1.5-14 processx_3.5.2
[43] rlang_1.0.1 GlobalOptions_0.1.2
[45] splines_4.1.2 broom_0.7.12
[47] yaml_2.2.2 reshape2_1.4.4
[49] abind_1.4-5 modelr_0.1.8
[51] crosstalk_1.2.0 backports_1.4.1
[53] httpuv_1.6.5 tools_4.1.2
[55] usethis_2.1.5 ellipsis_0.3.2
[57] jquerylib_0.1.4 biomformat_1.22.0
[59] BiocGenerics_0.40.0 sessioninfo_1.2.2
[61] plyr_1.8.6 zlibbioc_1.40.0
[63] RCurl_1.98-1.6 ps_1.6.0
[65] prettyunits_1.1.1 GetoptLong_1.0.5
[67] S4Vectors_0.32.3 SummarizedExperiment_1.22.0 [69] haven_2.4.3 ggrepel_0.9.1
[71] cluster_2.1.2 fs_1.5.2
[73] magrittr_2.0.2 data.table_1.14.2
[75] circlize_0.4.14 reprex_2.0.1
[77] matrixStats_0.61.0 pkgload_1.2.4
[79] hms_1.1.1 mime_0.12
[81] xtable_1.8-4 jpeg_0.1-9
[83] readxl_1.3.1 IRanges_2.28.0
[85] gridExtra_2.3 shape_1.4.6
[87] testthat_3.1.2 compiler_4.1.2
[89] crayon_1.4.2 htmltools_0.5.2
[91] mgcv_1.8-38 later_1.3.0
[93] tzdb_0.2.0 RcppParallel_5.1.5
[95] lubridate_1.8.0 DBI_1.1.2
[97] dbplyr_2.1.1 MASS_7.3-55
[99] ShortRead_1.50.0 Matrix_1.4-0
[101] ade4_1.7-18 car_3.0-12
[103] brio_1.1.3 cli_3.1.1
[105] parallel_4.1.2 igraph_1.2.11
[107] GenomicRanges_1.44.0 pkgconfig_2.0.3
[109] GenomicAlignments_1.28.0 registry_0.5-1
[111] xml2_1.3.3 foreach_1.5.2
[113] bslib_0.3.1 multtest_2.50.0
[115] XVector_0.34.0 rvest_1.0.2
[117] callr_3.7.0 digest_0.6.29
[119] Biostrings_2.62.0 cellranger_1.1.0
[121] curl_4.3.2 Rsamtools_2.8.0
[123] rjson_0.2.21 lifecycle_1.0.1
[125] nlme_3.1-155 jsonlite_1.7.3
[127] Rhdf5lib_1.16.0 carData_3.0-5
[129] desc_1.4.0 fansi_1.0.2
[131] pillar_1.7.0 fastmap_1.1.0
[133] httr_1.4.2 pkgbuild_1.3.1
[135] survival_3.2-13 glue_1.6.1
[137] remotes_2.4.2 png_0.1-7
[139] iterators_1.0.14 stringi_1.7.6
[141] sass_0.4.0 latticeExtra_0.6-29
[143] memoise_2.0.1 ape_5.6-1