ggordiplots - Make 'ggplot2' Versions of Vegan's Ordiplots

The 'vegan' package includes several functions for adding features to ordination plots: ordiarrows(), ordiellipse(), ordihull(), ordispider() and ordisurf(). This package adds these same features to ordination plots made with 'ggplot2'. In addition, gg_ordibubble() sizes points relative to the value of an environmental variable.

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6.23 score 8 stars 213 scripts 487 downloads

QsRutils - R Functions Useful for Community Ecology

A collection of utility functions for community ecology analyses, with emphasis on workflows using the 'phyloseq' and 'vegan' packages. Includes functions for normalizing OTU tables, computing alpha diversity via rarefaction (using a fast C++ implementation), differential abundance comparisons with compact letter displays, primer checking for amplicon sequencing, plotting QIIME 2/DADA2 generated transition stats and miscellaneous helpers for ordination plots and taxonomic name formatting.

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cpp

5.92 score 3 stars 31 scripts

QsRutils - R Functions Useful for Community Ecology

A collection of utility functions for community ecology analyses, with emphasis on workflows using the 'phyloseq' and 'vegan' packages. Includes functions for normalizing OTU tables, computing alpha diversity via rarefaction (using a fast C++ implementation), differential abundance comparisons with compact letter displays, primer checking for amplicon sequencing, plotting QIIME 2/DADA2 generated transition stats and miscellaneous helpers for ordination plots and taxonomic name formatting.

Last updated

cpp

3.49 score 31 scripts

speedytax - Rapidly Import Classifier Results into 'phyloseq'

Import classification results from the 'RDP Classifier' (Ribosomal Database Project),' 'USEARCH sintax,' 'vsearch sintax' and the 'QIIME2' (Quantitative Insights into Microbial Ecology) classifiers into 'phyloseq' tax_table objects.

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cpp

2.70 score 7 scripts 172 downloads