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update readme, fix runiverse badge and ggplot deprecation notices
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david-barnett committed Jun 30, 2024
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9 changes: 4 additions & 5 deletions README.Rmd
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Expand Up @@ -23,13 +23,12 @@ citations <- paste0("~", stringr::str_extract(rvest::html_text(citeElem), "[0-9]
# microViz <a href='https://david-barnett.github.io/microViz/index.html'><img src="man/figures/logo.png" align="right" height="180" width="156"/></a>

<!-- badges: start -->

[![R-CMD-check](https://github.com/david-barnett/microViz/workflows/R-CMD-check/badge.svg)](https://github.com/david-barnett/microViz/actions)
[![codecov](https://codecov.io/gh/david-barnett/microViz/branch/main/graph/badge.svg?token=C1EoVkhnxA)](https://codecov.io/gh/david-barnett/microViz)
![GitHub R package version](https://img.shields.io/github/r-package/v/david-barnett/microViz?label=Latest)
![GitHub release (including pre-releases)](https://img.shields.io/github/v/release/david-barnett/microViz?include_prereleases&label=Release)
![Docker Image Version (latest by date)](https://img.shields.io/docker/v/barnettdavid/microviz-rocker-verse?color=blue&label=Docker)
[![r-universe microViz status](https://david-barnett.r-universe.dev/badges/microViz)](https://david-barnett.r-universe.dev/ui#package:microViz)
[![microViz status 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-`r citations`-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)
Expand Down Expand Up @@ -307,10 +306,10 @@ perm2 %>%
max_angle = 90, size = 3, aspect_ratio = 0.8, colour = "black"
)
) +
stat_ellipse(aes(colour = nationality), linewidth = 0.2) + # linewidth not size since ggplot 3.4.0
scale_color_brewer(palette = "Set1") +
stat_ellipse(aes(colour = nationality), linewidth = 0.2) +
scale_color_brewer(palette = "Set1", guide = guide_legend(position = "inside")) +
coord_fixed(ratio = 0.8, clip = "off", xlim = c(-4, 4)) +
theme(legend.position = c(0.9, 0.1), legend.background = element_rect())
theme(legend.position.inside = c(0.9, 0.1), legend.background = element_rect())
```

### Correlation Heatmaps
Expand Down
41 changes: 18 additions & 23 deletions README.md
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Expand Up @@ -13,8 +13,8 @@ version](https://img.shields.io/github/r-package/v/david-barnett/microViz?label=
pre-releases)](https://img.shields.io/github/v/release/david-barnett/microViz?include_prereleases&label=Release)
![Docker Image Version (latest by
date)](https://img.shields.io/docker/v/barnettdavid/microviz-rocker-verse?color=blue&label=Docker)
[![r-universe microViz
status](https://david-barnett.r-universe.dev/badges/microViz)](https://david-barnett.r-universe.dev/ui#package:microViz)
[![microViz status
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-~135-blueviolet)](https://scholar.google.com/scholar?hl=en&as_sdt=2005&sciodt=0,5&cites=5439940108464463894&scipsc=&q=&scisbd=1)
Expand Down Expand Up @@ -150,7 +150,7 @@ test this.

``` r
library(microViz)
#> microViz version 0.12.3 - Copyright (C) 2021-2024 David Barnett
#> microViz version 0.12.3.9000 - 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"
)
#> 2024-06-06 20:28:23.195662 - Starting PERMANOVA with 99 perms with 1 processes
#> 2024-06-06 20:28:23.252764 - Finished PERMANOVA
#> 2024-06-30 10:55:51.862638 - Starting PERMANOVA with 99 perms with 1 processes
#> 2024-06-30 10:55:51.919099 - Finished PERMANOVA
```

``` r
Expand Down Expand Up @@ -348,8 +348,8 @@ 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
#> 2024-06-06 20:28:23.263874 - Starting PERMANOVA with 999 perms with 1 processes
#> 2024-06-06 20:28:24.92056 - Finished PERMANOVA
#> 2024-06-30 10:55:51.930319 - Starting PERMANOVA with 999 perms with 1 processes
#> 2024-06-30 10:55:53.574252 - Finished PERMANOVA
```

We’ll visualise the effect of nationality and bodyweight on sample
Expand All @@ -367,21 +367,15 @@ perm2 %>%
max_angle = 90, size = 3, aspect_ratio = 0.8, colour = "black"
)
) +
stat_ellipse(aes(colour = nationality), linewidth = 0.2) + # linewidth not size since ggplot 3.4.0
scale_color_brewer(palette = "Set1") +
stat_ellipse(aes(colour = nationality), linewidth = 0.2) +
scale_color_brewer(palette = "Set1", guide = guide_legend(position = "inside")) +
coord_fixed(ratio = 0.8, clip = "off", xlim = c(-4, 4)) +
theme(legend.position = c(0.9, 0.1), legend.background = element_rect())
theme(legend.position.inside = c(0.9, 0.1), legend.background = element_rect())
#>
#> Centering (mean) and scaling (sd) the constraints and/or conditions:
#> weight
#> african
#> female
#> Warning: A numeric `legend.position` argument in `theme()` was deprecated in ggplot2
#> 3.5.0.
#> ℹ Please use the `legend.position.inside` argument of `theme()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
```

<img src="man/figures/README-constrained-ord-plot-1.png" width="100%" />
Expand Down Expand Up @@ -467,8 +461,9 @@ sessionInfo()
#> [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_0.12.3
#> [5] testthat_3.2.1.1 devtools_2.4.5 usethis_2.2.3
#> [1] ggplot2_3.5.1 dplyr_1.1.4 phyloseq_1.48.0
#> [4] microViz_0.12.3.9000 testthat_3.2.1.1 devtools_2.4.5
#> [7] usethis_2.2.3
#>
#> loaded via a namespace (and not attached):
#> [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8
Expand All @@ -482,7 +477,7 @@ sessionInfo()
#> [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_1.8.1.1
#> [34] digest_0.6.35 selectr_0.4-2 colorspace_2.1-0
#> [34] digest_0.6.36 selectr_0.4-2 colorspace_2.1-0
#> [37] S4Vectors_0.42.0 ps_1.7.6 pkgload_1.3.4
#> [40] seriation_1.5.5 vegan_2.6-6.1 labeling_0.4.3
#> [43] fansi_1.0.6 httr_1.4.7 mgcv_1.9-1
Expand All @@ -504,15 +499,15 @@ sessionInfo()
#> [91] lattice_0.22-6 survival_3.5-8 tidyselect_1.2.1
#> [94] registry_0.5-1 ComplexHeatmap_2.20.0 Biostrings_2.72.0
#> [97] miniUI_0.1.1.1 knitr_1.47 gridExtra_2.3
#> [100] IRanges_2.38.0 stats4_4.4.0 xfun_0.44
#> [100] IRanges_2.38.0 stats4_4.4.0 xfun_0.45
#> [103] Biobase_2.64.0 matrixStats_1.3.0 brio_1.1.5
#> [106] stringi_1.8.4 UCSC.utils_1.0.0 yaml_2.3.8
#> [109] evaluate_0.23 codetools_0.2-20 tibble_3.2.1
#> [112] cli_3.6.2 xtable_1.8-4 munsell_0.5.1
#> [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_1.0.12 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_1.5.2
#> [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
```

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