From 1dadd117bd3c5bd724c0be66e9572b4aa6443191 Mon Sep 17 00:00:00 2001 From: David Barnett Date: Mon, 16 Dec 2024 09:49:23 +0000 Subject: [PATCH] 0.12.6 version bump --- DESCRIPTION | 2 +- NEWS.md | 4 +- README.md | 97 ++++++++++++++++----------------- vignettes/web-only/heatmaps.Rmd | 2 +- 4 files changed, 53 insertions(+), 52 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 90a0aa9c..c52d915a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: microViz Title: Microbiome Data Analysis and Visualization -Version: 0.12.5.9000 +Version: 0.12.6 Authors@R: person(given = "David", family = "Barnett", diff --git a/NEWS.md b/NEWS.md index 283327c8..c0a5a534 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,6 @@ -# microViz (development version) +# microViz 0.12.6 + +- Fix: `ord_plot` score retrieval is now compatible with vegan 2.7.0 # microViz 0.12.5 diff --git a/README.md b/README.md index d7a30ad6..1f9e4690 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ date)](https://img.shields.io/docker/v/barnettdavid/microviz-rocker-verse?color= badge](https://david-barnett.r-universe.dev/badges/microViz)](https://david-barnett.r-universe.dev/microViz) [![JOSS article](https://joss.theoj.org/papers/4547b492f224a26d96938ada81fee3fa/status.svg)](https://joss.theoj.org/papers/4547b492f224a26d96938ada81fee3fa) -[![Citations](https://img.shields.io/badge/Citations-~193-blueviolet)](https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0,5&cites=5439940108464463894&scipsc=&q=&scisbd=1) +[![Citations](https://img.shields.io/badge/Citations-~205-blueviolet)](https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0,5&cites=5439940108464463894&scipsc=&q=&scisbd=1) [![Zenodo DOI](https://zenodo.org/badge/307119750.svg)](https://zenodo.org/badge/latestdoi/307119750) @@ -150,7 +150,7 @@ test this. ``` r library(microViz) -#> microViz version 0.12.5 - Copyright (C) 2021-2024 David Barnett +#> microViz version 0.12.6 - Copyright (C) 2021-2024 David Barnett #> ! Website: https://david-barnett.github.io/microViz #> ✔ Useful? For citation details, run: `citation("microViz")` #> ✖ Silence? `suppressPackageStartupMessages(library(microViz))` @@ -316,8 +316,8 @@ aitchison_perm <- aitchison_dists %>% n_processes = 1, n_perms = 99, # you should use at least 999! variables = "bmi_group" ) -#> 2024-11-18 15:43:00.162228 - Starting PERMANOVA with 99 perms with 1 processes -#> 2024-11-18 15:43:00.240951 - Finished PERMANOVA +#> 2024-12-16 09:47:30.753936 - Starting PERMANOVA with 99 perms with 1 processes +#> 2024-12-16 09:47:30.829263 - Finished PERMANOVA # view the permanova results perm_get(aitchison_perm) %>% as.data.frame() @@ -342,8 +342,8 @@ your permanova directly using the `ord_plot` function with constraints perm2 <- aitchison_dists %>% dist_permanova(variables = c("weight", "african", "sex"), seed = 321) #> Dropping samples with missings: 2 -#> 2024-11-18 15:43:00.255258 - Starting PERMANOVA with 999 perms with 1 processes -#> 2024-11-18 15:43:02.429889 - Finished PERMANOVA +#> 2024-12-16 09:47:30.844906 - Starting PERMANOVA with 999 perms with 1 processes +#> 2024-12-16 09:47:33.254138 - Finished PERMANOVA ``` We’ll visualise the effect of nationality and bodyweight on sample @@ -434,9 +434,9 @@ and by participating in this project you agree to abide by its terms. ``` r sessionInfo() -#> R version 4.4.0 (2024-04-24) +#> R version 4.4.2 (2024-10-31) #> Platform: aarch64-apple-darwin20 -#> Running under: macOS Sonoma 14.7 +#> Running under: macOS Sequoia 15.1.1 #> #> Matrix products: default #> BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib @@ -445,59 +445,58 @@ sessionInfo() #> locale: #> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 #> -#> time zone: Europe/Amsterdam +#> time zone: Europe/London #> tzcode source: internal #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: -#> [1] ggplot2_3.5.1 dplyr_1.1.4 phyloseq_1.48.0 microViz_0.12.5 -#> [5] testthat_3.2.1.1 devtools_2.4.5 usethis_3.0.0 +#> [1] ggplot2_3.5.1 dplyr_1.1.4 phyloseq_1.48.0 microViz_0.12.6 +#> [5] testthat_3.2.2 devtools_2.4.5 usethis_3.1.0 #> #> loaded via a namespace (and not attached): -#> [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 +#> [1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.8.9 #> [4] shape_1.4.6.1 magrittr_2.0.3 farver_2.1.2 -#> [7] rmarkdown_2.27 GlobalOptions_0.1.2 fs_1.6.4 +#> [7] rmarkdown_2.29 GlobalOptions_0.1.2 fs_1.6.5 #> [10] zlibbioc_1.50.0 vctrs_0.6.5 multtest_2.60.0 #> [13] memoise_2.0.1 Cairo_1.6-2 htmltools_0.5.8.1 -#> [16] curl_5.2.1 Rhdf5lib_1.26.0 rhdf5_2.48.0 +#> [16] curl_6.0.1 Rhdf5lib_1.26.0 rhdf5_2.48.0 #> [19] htmlwidgets_1.6.4 plyr_1.8.9 cachem_1.1.0 -#> [22] commonmark_1.9.1 igraph_2.0.3 mime_0.12 +#> [22] commonmark_1.9.2 igraph_2.1.2 mime_0.12 #> [25] lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3 -#> [28] Matrix_1.7-0 R6_2.5.1 fastmap_1.2.0 -#> [31] clue_0.3-65 GenomeInfoDbData_1.2.12 shiny_1.9.1 -#> [34] digest_0.6.36 selectr_0.4-2 colorspace_2.1-1 -#> [37] S4Vectors_0.42.1 ps_1.7.7 pkgload_1.4.0 -#> [40] seriation_1.5.5 vegan_2.6-8 labeling_0.4.3 +#> [28] Matrix_1.7-1 R6_2.5.1 fastmap_1.2.0 +#> [31] clue_0.3-66 GenomeInfoDbData_1.2.12 shiny_1.10.0 +#> [34] digest_0.6.37 selectr_0.4-2 colorspace_2.1-1 +#> [37] S4Vectors_0.42.1 ps_1.8.1 pkgload_1.4.0 +#> [40] seriation_1.5.7 vegan_2.7-0 labeling_0.4.3 #> [43] fansi_1.0.6 httr_1.4.7 mgcv_1.9-1 -#> [46] compiler_4.4.0 remotes_2.5.0 doParallel_1.0.17 -#> [49] withr_3.0.1 viridis_0.6.5 pkgbuild_1.4.4 -#> [52] highr_0.11 MASS_7.3-61 sessioninfo_1.2.2 -#> [55] rjson_0.2.22 biomformat_1.32.0 permute_0.9-7 -#> [58] tools_4.4.0 chromote_0.2.0 ape_5.8 -#> [61] httpuv_1.6.15 glue_1.8.0 nlme_3.1-165 -#> [64] rhdf5filters_1.16.0 promises_1.3.0 gridtext_0.1.5 -#> [67] grid_4.4.0 Rtsne_0.17 cluster_2.1.6 -#> [70] reshape2_1.4.4 ade4_1.7-22 generics_0.1.3 -#> [73] gtable_0.3.5 microbiome_1.26.0 ca_0.71.1 -#> [76] tidyr_1.3.1 websocket_1.4.2 data.table_1.15.4 -#> [79] xml2_1.3.6 utf8_1.2.4 XVector_0.44.0 -#> [82] BiocGenerics_0.50.0 markdown_1.13 foreach_1.5.2 -#> [85] pillar_1.9.0 stringr_1.5.1 later_1.3.2 -#> [88] circlize_0.4.16 splines_4.4.0 ggtext_0.1.2 -#> [91] lattice_0.22-6 survival_3.7-0 tidyselect_1.2.1 -#> [94] registry_0.5-1 ComplexHeatmap_2.20.0 Biostrings_2.72.1 -#> [97] miniUI_0.1.1.1 knitr_1.48 gridExtra_2.3 -#> [100] IRanges_2.38.1 stats4_4.4.0 xfun_0.46 -#> [103] Biobase_2.64.0 matrixStats_1.3.0 brio_1.1.5 -#> [106] stringi_1.8.4 UCSC.utils_1.0.0 yaml_2.3.10 -#> [109] evaluate_0.24.0 codetools_0.2-20 tibble_3.2.1 -#> [112] cli_3.6.3 xtable_1.8-4 munsell_0.5.1 -#> [115] processx_3.8.4 Rcpp_1.0.13 GenomeInfoDb_1.40.1 -#> [118] png_0.1-8 parallel_4.4.0 ellipsis_0.3.2 -#> [121] profvis_0.3.8 urlchecker_1.0.1 viridisLite_0.4.2 -#> [124] scales_1.3.0 purrr_1.0.2 crayon_1.5.3 -#> [127] GetoptLong_1.0.5 rlang_1.1.4 TSP_1.2-4 -#> [130] rvest_1.0.4 +#> [46] compiler_4.4.2 remotes_2.5.0 withr_3.0.2 +#> [49] doParallel_1.0.17 viridis_0.6.5 pkgbuild_1.4.5 +#> [52] MASS_7.3-61 sessioninfo_1.2.2 rjson_0.2.23 +#> [55] biomformat_1.32.0 permute_0.9-7 tools_4.4.2 +#> [58] chromote_0.3.1 ape_5.8 httpuv_1.6.15 +#> [61] glue_1.8.0 nlme_3.1-166 rhdf5filters_1.16.0 +#> [64] promises_1.3.2 gridtext_0.1.5 grid_4.4.2 +#> [67] Rtsne_0.17 cluster_2.1.8 reshape2_1.4.4 +#> [70] ade4_1.7-22 generics_0.1.3 gtable_0.3.6 +#> [73] microbiome_1.26.0 ca_0.71.1 tidyr_1.3.1 +#> [76] websocket_1.4.2 data.table_1.16.4 xml2_1.3.6 +#> [79] utf8_1.2.4 XVector_0.44.0 BiocGenerics_0.50.0 +#> [82] markdown_1.13 foreach_1.5.2 pillar_1.9.0 +#> [85] stringr_1.5.1 later_1.4.1 circlize_0.4.16 +#> [88] splines_4.4.2 ggtext_0.1.2 lattice_0.22-6 +#> [91] survival_3.7-0 tidyselect_1.2.1 registry_0.5-1 +#> [94] ComplexHeatmap_2.20.0 Biostrings_2.72.1 miniUI_0.1.1.1 +#> [97] knitr_1.49 gridExtra_2.3 IRanges_2.38.1 +#> [100] stats4_4.4.2 xfun_0.49 Biobase_2.64.0 +#> [103] matrixStats_1.4.1 brio_1.1.5 stringi_1.8.4 +#> [106] UCSC.utils_1.0.0 yaml_2.3.10 evaluate_1.0.1 +#> [109] codetools_0.2-20 tibble_3.2.1 cli_3.6.3 +#> [112] xtable_1.8-4 munsell_0.5.1 processx_3.8.4 +#> [115] Rcpp_1.0.13-1 GenomeInfoDb_1.40.1 png_0.1-8 +#> [118] parallel_4.4.2 ellipsis_0.3.2 profvis_0.4.0 +#> [121] urlchecker_1.0.1 viridisLite_0.4.2 scales_1.3.0 +#> [124] purrr_1.0.2 crayon_1.5.3 GetoptLong_1.0.5 +#> [127] rlang_1.1.4 TSP_1.2-4 rvest_1.0.4 ``` diff --git a/vignettes/web-only/heatmaps.Rmd b/vignettes/web-only/heatmaps.Rmd index 93c606db..f1450e57 100644 --- a/vignettes/web-only/heatmaps.Rmd +++ b/vignettes/web-only/heatmaps.Rmd @@ -575,7 +575,7 @@ correlations_df %>% )) ``` -Additionally, with the `scale_y_dendrogram` function from the [ggh4x package](https://teunbrand.github.io/ggh4x) you can add a visualisation of the hclust dendrogram to the y axis. See: +Additionally, with the `scale_y_dendro` function from the [legendry package](https://teunbrand.github.io/legendry) you can add a visualisation of the hclust dendrogram to the y axis. See: ## Other stuff