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david-barnett committed Oct 20, 2022
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: microViz
Title: Microbiome Data Analysis and Visualization
Version: 0.9.6.9027
Version: 0.9.7
Authors@R:
person(given = "David",
family = "Barnett",
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4 changes: 2 additions & 2 deletions NEWS.md
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# microViz (development version)
# microViz 0.9.7

## Features

- `ps_seriate` can now aggregate taxa before seriation (returns unaggregated still)
- `comp_barplot` gains x argument, to change default x aesthetic to something other than SAMPLE,
which is useful for (faceted) plotting of repeated samples from the same site/individual
over time or in different conditions when some samples are missing (see compositions tutorial article)
- `ps_seriate` can now aggregate taxa before seriation (returns unaggregated still)

# microViz 0.9.6

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96 changes: 46 additions & 50 deletions README.md
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Expand Up @@ -138,7 +138,7 @@ formally test this.
``` r
library(microViz)
#>
#> microViz version 0.9.6.9020 - Copyright (C) 2022 David Barnett
#> microViz version 0.9.7 - Copyright (C) 2022 David Barnett
#> * Website: https://david-barnett.github.io/microViz/
#> * Useful? For citation info, run: citation('microViz')
#> * Silence: suppressPackageStartupMessages(library(microViz))
Expand Down Expand Up @@ -321,8 +321,8 @@ aitchison_perm <- aitchison_dists %>%
n_processes = 1, n_perms = 99, # you should use at least 999!
variables = "bmi_group"
)
#> 2022-10-18 11:26:14 - Starting PERMANOVA with 99 perms with 1 processes
#> 2022-10-18 11:26:14 - Finished PERMANOVA
#> 2022-10-20 15:20:06 - Starting PERMANOVA with 99 perms with 1 processes
#> 2022-10-20 15:20:06 - Finished PERMANOVA

# view the permanova results
perm_get(aitchison_perm) %>% as.data.frame()
Expand Down Expand Up @@ -353,8 +353,8 @@ 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
#> 2022-10-18 11:26:14 - Starting PERMANOVA with 999 perms with 1 processes
#> 2022-10-18 11:26:16 - Finished PERMANOVA
#> 2022-10-20 15:20:06 - Starting PERMANOVA with 999 perms with 1 processes
#> 2022-10-20 15:20:08 - Finished PERMANOVA
```

We’ll visualise the effect of nationality and bodyweight on sample
Expand All @@ -377,7 +377,7 @@ perm2 %>%
coord_fixed(ratio = 0.35, clip = "off") +
theme(legend.position = c(0.9, 0.1), legend.background = element_rect())
#>
#> Centering (mean) and scaling (sd) the constraints and conditions:
#> Centering (mean) and scaling (sd) the constraints and/or conditions:
#> weight
#> african
#> female
Expand Down Expand Up @@ -447,12 +447,12 @@ and by participating in this project you agree to abide by its terms.
``` r
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Monterey 12.6
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
#> BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#>
#> locale:
#> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
Expand All @@ -461,54 +461,50 @@ sessionInfo()
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] ggplot2_3.3.6 dplyr_1.0.10 phyloseq_1.40.0
#> [4] microViz_0.9.6.9020 testthat_3.1.5 devtools_2.4.5
#> [7] usethis_2.1.6
#> [1] ggplot2_3.3.6 dplyr_1.0.10 phyloseq_1.40.0 microViz_0.9.7
#> [5] testthat_3.1.4 devtools_2.4.3 usethis_2.1.6
#>
#> loaded via a namespace (and not attached):
#> [1] circlize_0.4.15 plyr_1.8.7 igraph_1.3.5
#> [4] selectr_0.4-2 splines_4.2.1 GenomeInfoDb_1.32.4
#> [7] digest_0.6.29 foreach_1.5.2 htmltools_0.5.3
#> [10] magick_2.7.3 viridis_0.6.2 fansi_1.0.3
#> [7] digest_0.6.30 foreach_1.5.2 htmltools_0.5.3
#> [10] viridis_0.6.2 magick_2.7.3 fansi_1.0.3
#> [13] magrittr_2.0.3 memoise_2.0.1 cluster_2.1.3
#> [16] doParallel_1.0.17 remotes_2.4.2 ComplexHeatmap_2.12.1
#> [19] Biostrings_2.64.0 matrixStats_0.62.0 prettyunits_1.1.1
#> [22] colorspace_2.0-3 corncob_0.3.0 rvest_1.0.2
#> [25] xfun_0.31 callr_3.7.2 crayon_1.5.2
#> [19] Biostrings_2.64.1 matrixStats_0.62.0 prettyunits_1.1.1
#> [22] colorspace_2.0-3 corncob_0.2.0 rvest_1.0.3
#> [25] xfun_0.31 callr_3.7.0 crayon_1.5.2
#> [28] RCurl_1.98-1.9 jsonlite_1.8.2 survival_3.3-1
#> [31] iterators_1.0.14 ape_5.6-2 glue_1.6.2
#> [34] registry_0.5-1 gtable_0.3.1 zlibbioc_1.42.0
#> [37] XVector_0.36.0 GetoptLong_1.0.5 pkgbuild_1.3.1
#> [40] Rhdf5lib_1.18.0 shape_1.4.6 BiocGenerics_0.42.0
#> [43] scales_1.2.1 DBI_1.1.2 miniUI_0.1.1.1
#> [46] Rcpp_1.0.9 gridtext_0.1.5 viridisLite_0.4.1
#> [49] xtable_1.8-4 clue_0.3-61 stats4_4.2.1
#> [52] profvis_0.3.7 htmlwidgets_1.5.4 httr_1.4.3
#> [55] RColorBrewer_1.1-3 ellipsis_0.3.2 urlchecker_1.0.1
#> [58] pkgconfig_2.0.3 farver_2.1.1 utf8_1.2.2
#> [61] tidyselect_1.2.0 labeling_0.4.2 rlang_1.0.6
#> [64] reshape2_1.4.4 later_1.3.0 munsell_0.5.0
#> [67] tools_4.2.1 cachem_1.0.6 cli_3.4.1
#> [70] generics_0.1.3 ade4_1.7-19 evaluate_0.15
#> [73] biomformat_1.24.0 stringr_1.4.1 fastmap_1.1.0
#> [76] yaml_2.3.5 processx_3.7.0 knitr_1.40
#> [79] fs_1.5.2 purrr_0.3.5 nlme_3.1-157
#> [82] mime_0.12 xml2_1.3.3 brio_1.1.3
#> [85] compiler_4.2.1 rstudioapi_0.14 curl_4.3.2
#> [88] png_0.1-7 tibble_3.1.8 stringi_1.7.8
#> [91] highr_0.9 ps_1.7.0 lattice_0.20-45
#> [94] Matrix_1.4-1 markdown_1.1 vegan_2.6-4
#> [97] microbiome_1.18.0 permute_0.9-7 multtest_2.52.0
#> [100] vctrs_0.4.2 pillar_1.8.1 lifecycle_1.0.3
#> [103] rhdf5filters_1.8.0 GlobalOptions_0.1.2 data.table_1.14.2
#> [106] bitops_1.0-7 seriation_1.3.6.9000 httpuv_1.6.6
#> [109] R6_2.5.1 promises_1.2.0.1 TSP_1.2-1
#> [112] gridExtra_2.3 IRanges_2.30.0 sessioninfo_1.2.2
#> [115] codetools_0.2-18 MASS_7.3-57 assertthat_0.2.1
#> [118] pkgload_1.3.0 rhdf5_2.40.0 rjson_0.2.21
#> [121] withr_2.5.0 S4Vectors_0.34.0 GenomeInfoDbData_1.2.8
#> [124] ggtext_0.1.2 mgcv_1.8-40 parallel_4.2.1
#> [127] grid_4.2.1 tidyr_1.2.1 rmarkdown_2.16
#> [130] Cairo_1.6-0 Rtsne_0.16 Biobase_2.56.0
#> [133] shiny_1.7.2
#> [40] Rhdf5lib_1.18.2 shape_1.4.6 BiocGenerics_0.42.0
#> [43] scales_1.2.1 DBI_1.1.3 Rcpp_1.0.9
#> [46] viridisLite_0.4.1 gridtext_0.1.4 clue_0.3-62
#> [49] stats4_4.2.1 httr_1.4.3 RColorBrewer_1.1-3
#> [52] ellipsis_0.3.2 pkgconfig_2.0.3 farver_2.1.1
#> [55] utf8_1.2.2 tidyselect_1.2.0 labeling_0.4.2
#> [58] rlang_1.0.6 reshape2_1.4.4 munsell_0.5.0
#> [61] tools_4.2.1 cachem_1.0.6 cli_3.4.1
#> [64] generics_0.1.3 ade4_1.7-19 evaluate_0.15
#> [67] biomformat_1.24.0 stringr_1.4.1 fastmap_1.1.0
#> [70] yaml_2.3.6 processx_3.5.3 knitr_1.39
#> [73] fs_1.5.2 purrr_0.3.5 nlme_3.1-157
#> [76] xml2_1.3.3 brio_1.1.3 compiler_4.2.1
#> [79] rstudioapi_0.13 curl_4.3.2 png_0.1-7
#> [82] tibble_3.1.8 stringi_1.7.8 highr_0.9
#> [85] ps_1.7.0 desc_1.4.1 lattice_0.20-45
#> [88] Matrix_1.4-1 markdown_1.1 vegan_2.6-4
#> [91] microbiome_1.18.0 permute_0.9-7 multtest_2.52.0
#> [94] vctrs_0.4.2 pillar_1.8.1 lifecycle_1.0.3
#> [97] rhdf5filters_1.8.0 GlobalOptions_0.1.2 data.table_1.14.4
#> [100] bitops_1.0-7 seriation_1.3.6 R6_2.5.1
#> [103] TSP_1.2-1 gridExtra_2.3 IRanges_2.30.1
#> [106] sessioninfo_1.2.2 codetools_0.2-18 MASS_7.3-57
#> [109] assertthat_0.2.1 pkgload_1.2.4 rhdf5_2.40.0
#> [112] rprojroot_2.0.3 rjson_0.2.21 withr_2.5.0
#> [115] S4Vectors_0.34.0 GenomeInfoDbData_1.2.8 mgcv_1.8-40
#> [118] parallel_4.2.1 ggtext_0.1.1 grid_4.2.1
#> [121] tidyr_1.2.1 rmarkdown_2.14 Cairo_1.5-15
#> [124] Rtsne_0.16 Biobase_2.56.0
```

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