Package index
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palette_jak() - A full-service color palette creator
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show_color_palette() - showColorPalette
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show_all_color_palettes() - Show all color palettes in the jak_palettes object
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expand_named_palette() - Expanded Color Palette with Names
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get_phylo_palette() - getPhyloPalette
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jak_palettes - Color Palettes
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get_alpha_diversity() - Alpha-Diversity Measures
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get_phylo_diversity() - Phylogenetic Diversity Measures
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permanova() - Permanova (adonis) and visualization
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pairwiseAdonis() - Calculate Total and Pairwise Adonis Values
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phylo_other() - Combine low-abundant taxa into a single category
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plot_distances() - Boxplot of Beta-diversity Distances
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plotPD() - Plot Faith's PD
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zeroOTU() - Sets ASV abundance values below x to zero
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fastq_filter_summary_amplicon() - Summarize a fastq_filter.py file in amplicon mode
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fastq_filter_summary_meta() - Summarize a fastq_filter.py file in metagenome mode
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fastq_info_summary() - Summarize a fastq_info file
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run_fts() - run_fts
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get_fts_intervals() - Get intervals for a run_fts() dataframe
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plot_fts_intervals() - Plot intervals for a run_fts() dataframe
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plot_fts_points() - Plot points for a run_fts() dataframe
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getSig() - getSig
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sigCombine() - Combine DESeq sigtab contrasts
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orthofinder_complete_clusters() - Summarize single copy and orthogroups found in all
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orthofinder_summary() - Summarize an orthofinder TSV file
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drep_extract() - Extract dRep genome results
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seqtab_stats() - Extract DADA2 seqtab statistics
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illumina_codes() - Get Illumina machine and flow cell code from run id