phyloseq alpha diversity

with method-specific error-bars. See Also

An experimentally meaningful categorical variable is usually a good choice – in this case, the "SampleType" variable works much better than attempting to interpret the sample names directly (as in the previous plot): Now suppose we wanted to use an external variable in the plot that isn’t in the GP dataset already – for example, a logical that indicated whether or not the samples are human-associated. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. meaning that all plot panels will be placed in a single row, Values must be among those supported: all available alpha-diversity measures will be included in plot panels. The PhyloSeq homepage provides additional vignettes which go beyond what is presented below. Ideally, published scientific analyses are completely reproducible in as easy a fashion as possible; and anything less represents an impediment to both progress and peer review ( Peng, 2011 ). I find this kind of distracting, and doesn’t add any information or clarity.

side-by-side. ## There are many more interesting examples at the phyloseq online tutorials. Some of these methods depend on data transformations (e.g.

chosen automatically (wrapped) based on the number of panels A typical workflow in Shiny-phyloseq begins with data upload and selection, followed by optional filtering of Operational Taxonomic Units (OTUs) or samples.


Strictly speaking, this function is not only estimating richness, despite its name. © The Author 2014. the distance measurement algorithm to use from “manhattan”, “euclidean”, “canberra”, “bray”, similar to selecting the number of neighbors to consider in decision making (should not be bigger than 3 * perplexity < nrow(X) - 1, see Rtsne for interpretation). of the variable name in

To make this work, you need to download and import the dummy dataset described in chapter ”Phyloseq Help”.

This argument is passed to facet_wrap.


The plot generated by this function will include every sample The name of this function may be changed in future versions to reflect this and avoid confusion. First, merge the samples. Usage

This can be a vector of multiple factors to subset on. and returns the results as a data.frame. variable in sample_data Values must be among those supported:

cores numeric value for number of CPU cores to use for the pair-wise permutations. Pre-loaded datasets are available by default, and users can optionally specify public datasets hosted on QIIME-DB ( Caporaso et al. be used in all panels. We recently described a software package for the R language, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data ( McMurdie and Holmes, 2013 ). Now tell plot_richness to map the new human variable on the horizontal axis, and shade the points in different color groups, according to which "SampleType" they belong. Finally, a user can download a compressed file containing the complete code and data necessary to completely reproduce the steps that led to their graphical result.

Computes the correlation of numerical variables with taxa and graphs as heatmap. in the dataset (nsamples(physeq)). and have units of total taxa, and/or index value (dimensionless). estimate_richness, the variable names of that output should

The plot generated by this function will include every sample in physeq, but they …

Performs a number of standard alpha diversity estimates, and returns the results as a data.frame. Department of Statistics, Stanford University, Stanford, CA 94305, USA. or a custom supplied vector with length equal to the number of samples A ggplot plot object summarizing

despite its name.

We can avoid this by specifying a measures argument to plot_richness, which will include just the alpha-diversity measures that we want. Sort x-indices by the mean of one or more measures, A factor within the treatment. This set of plots is a lot of information.

Creates a ggplot object of the t-SNE ordination of the samples.

We can merge samples that are from the environment (SampleType), and make the points bigger with a ggplot2 layer.

Alpha diversity measures are used to identify within individual taxa richness and evenness. Like x, this can be a single character string of the variable name in later on if needed, just not before using this function. Alpha diversity describes the diversity in a sample or site. Or alternatively, pool all samples and Handling and analysis of high-throughput microbiome census data. No longer supported. (Optional).

or a custom supplied vector with length equal to the number of samples NOTE: Because this plotting function incorporates the output from Create a ggplot-object box-plot of the alpha-diversity from a phyloseq-object.

, 2008 ), QIIME ( Caporaso et al.

sample_data ... We will use the filtered phyloseq object from Set-up and Pre-processing section. colors | Name of a color set from the RColorBrewer package or a vector palete of R-accepted colors.

This is because they were the first layer, and our larger points are semi-transparent. (Required).

The vertical More demos of this package are available from the authors here. This D3 ( Bostock et al.

t-Distributed Tochastic Neighbor Embedding is a machine learning algorithm of nonlinear dimensionality reduction for high-dimensional data. I have 16 data for which I have generated alpha diversity data for using the estimate_richness function in phyloseq. This can be archived or shared for batch re-execution in R. The authors would like to thank Fatema AlGharbi, Brandon Ewonus and Shahriyar Pruisken for a summer pilot project exploring Shiny and phyloseq.

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