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0.12.6 version bump
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david-barnett committed Dec 16, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: microViz
Title: Microbiome Data Analysis and Visualization
Version: 0.12.5.9000
Version: 0.12.6
Authors@R:
person(given = "David",
family = "Barnett",
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4 changes: 3 additions & 1 deletion NEWS.md
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# microViz (development version)
# microViz 0.12.6

- Fix: `ord_plot` score retrieval is now compatible with vegan 2.7.0

# microViz 0.12.5

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97 changes: 48 additions & 49 deletions README.md
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Expand Up @@ -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)
<!-- badges: end -->
Expand Down Expand Up @@ -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))`
Expand Down Expand Up @@ -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()
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
```
2 changes: 1 addition & 1 deletion vignettes/web-only/heatmaps.Rmd
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Expand Up @@ -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: <https://teunbrand.github.io/ggh4x/articles/PositionGuides.html#dendrograms>
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: <https://teunbrand.github.io/legendry/reference/scale_y_dendro.html>


## Other stuff
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