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| output: github_document | ||
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| <!-- README.md is generated from README.Rmd. Please edit that file --> | ||
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| options(width = 100) | ||
| ``` | ||
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| # microViz <a href='https://david-barnett.github.io/microViz/index.html'><img src='man/figures/microViz-smaller.png' align="right" height="139" /></a> | ||
| # microViz <a href='https://david-barnett.github.io/microViz/index.html'><img src="man/figures/microViz-smaller.png" align="right" height="139"/></a> | ||
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| <!-- badges: start --> | ||
| [](https://github.com/david-barnett/microViz/actions) | ||
| [](https://codecov.io/gh/david-barnett/microViz) | ||
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| [](https://github.com/david-barnett/microViz/actions) [](https://codecov.io/gh/david-barnett/microViz) | ||
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| <!-- badges: end --> | ||
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| microViz provides functions for analysis and visualization of microbiome sequencing data. These functions are intended to be easy to use (with clear documentation) and modular (for extensibility and flexibility). | ||
| microViz provides functions for analysis and visualization of microbiome sequencing data. | ||
| These functions are intended to be easy to use and flexible. | ||
| microViz wraps, extends and complements popular microbial ecology packages like phyloseq, vegan, and microbiome. | ||
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| **See the documentation website for full details and examples:** https://david-barnett.github.io/microViz/ | ||
| **See the documentation website for full details and examples:** <https://david-barnett.github.io/microViz/> | ||
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| - The ["Get started"](https://david-barnett.github.io/microViz/articles/articles/microViz.html) page, and also [this ReadMe](https://david-barnett.github.io/microViz/index.html), show a few example analyses. | ||
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| - The [reference](https://david-barnett.github.io/microViz/reference/index.html) page lists all functions and links to their documentation and examples | ||
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| - Example video of [Interactive Shiny app](https://david-barnett.github.io/microViz/articles/articles/Interactive-Ordination.html) for exploring your ordination plots! | ||
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| - Other articles pages give tutorials and more complicated examples | ||
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| - [Working with phyloseq objects](https://david-barnett.github.io/microViz/articles/articles/phyloseq.html) | ||
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| - The ["Get started"](https://david-barnett.github.io/microViz/articles/articles/microViz.html) page, and also [this ReadMe](https://david-barnett.github.io/microViz/index.html), show a few example analyses. | ||
| - The [reference](https://david-barnett.github.io/microViz/reference/index.html) page lists all functions and links to their documentation and examples | ||
| - Example video of [Interactive Shiny app](https://david-barnett.github.io/microViz/articles/articles/Interactive-Ordination.html) for exploring your ordination plots! | ||
| - Other articles pages discuss and give tutorials and more complicated examples (coming soon!) | ||
| - The [changelog](https://david-barnett.github.io/microViz/news/index.html) describes important changes in new microViz package versions | ||
| - [Fixing your taxa table with tax_fix](https://david-barnett.github.io/microViz/articles/articles/tax-fixing.html) | ||
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| - [Visualising taxonomic compositions with customised barplots](https://david-barnett.github.io/microViz/articles/articles/Visualising-compositions.html) | ||
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| - (more coming soon! raise an issue on github if you have questions/requests) | ||
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| - The [changelog](https://david-barnett.github.io/microViz/news/index.html) describes important changes in new microViz package versions | ||
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| ## Installation | ||
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| You can install the latest available microViz package version using the following instructions. | ||
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| ``` r | ||
| # If you are on windows you will need to install RTools so that your computer can build this package | ||
| # If you are on Windows you will need to install RTools so that your computer can build this package | ||
| # Follow instructions here: http://jtleek.com/modules/01_DataScientistToolbox/02_10_rtools/ | ||
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| # If you are on macOS, you might need to install xquartz to make the heatmaps work (ComplexHeatmaps package) | ||
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| # # Installing the latest version of this package # # | ||
| devtools::install_github("david-barnett/[email protected]") # check 0.7.0 is the latest version? | ||
| # advanced tip: add @<commit-hash> after microViz to install a version from a particular commit | ||
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| ``` | ||
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| ## Examples below | ||
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| ) | ||
| ``` | ||
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| ## Example ordination plot workflow | ||
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| Maybe visually inspecting all your samples isn't quite what you want. | ||
| Ordination methods can also help you to visualise if overall microbial ecosystem composition differs markedly between groups, e.g. BMI. | ||
| Ordination methods can also help you to visualise if overall microbial ecosystem composition differs markedly between groups, e.g. | ||
| BMI. | ||
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| Here is one option to try first: | ||
| Here is one option to try first: | ||
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| 1. Filter out rare taxa (e.g. remove Genera not present in at least 10% of samples) - use `tax_filter()` | ||
| 2. Aggregate the taxa into bacterial families (for example) - use `tax_agg()` | ||
| 3. Transform the microbial data with the centre-log-ratio transformation - use `tax_transform()` | ||
| 4. Perform PCA with the clr-transformed features (equivalent to aitchison distance PCoA) - use `ord_calc()` | ||
| 5. Plot the first 2 axes of this PCA ordination, colouring samples by group and adding taxon loading arrows to visualise which taxa generally differ across your samples - use `ord_plot()` | ||
| 6. Customise the theme of the ggplot as you like and/or add features like ellipses or annotations | ||
| 1. Filter out rare taxa (e.g. remove Genera not present in at least 10% of samples) - use `tax_filter()` | ||
| 2. Aggregate the taxa into bacterial families (for example) - use `tax_agg()` | ||
| 3. Transform the microbial data with the centre-log-ratio transformation - use `tax_transform()` | ||
| 4. Perform PCA with the clr-transformed features (equivalent to aitchison distance PCoA) - use `ord_calc()` | ||
| 5. Plot the first 2 axes of this PCA ordination, colouring samples by group and adding taxon loading arrows to visualise which taxa generally differ across your samples - use `ord_plot()` | ||
| 6. Customise the theme of the ggplot as you like and/or add features like ellipses or annotations | ||
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| ```{r ordination-plot, dpi=300} | ||
| # perform ordination | ||
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| tax_agg("Family") %>% | ||
| tax_transform("clr") %>% | ||
| ord_calc() | ||
| # will automatically infer you want a "PCA" here | ||
| # ord_calc will automatically infer you want a "PCA" here | ||
| # specify explicitly with method = "PCA", or you can pick another method | ||
| # create plot | ||
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| ## PERMANOVA | ||
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| You visualised your ordinated data in the plot above. | ||
| You visualised your ordinated data in the plot above. | ||
| Below you can see how to perform a PERMANOVA to test the significance of BMI's association with overall microbial composition. | ||
| This example uses the Family-level aitchison distance to correspond with the plot above. | ||
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| cor_heatmap(psq, taxa, anno_tax = tax_anno(undetected = 50)) | ||
| ``` | ||
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| ## Session info | ||
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| ```{r} | ||
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