Package index
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read_orthogroups() - Import an orthofinder TSV file
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orthogroup_list2counts() - Convert an orthogroup list dataframe to a count dataframe
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get_alpha_diversity() - Alpha-Diversity Measures
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get_alpha_S() - Calculate richness (S) and sample depth
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get_alpha_simpson() - Calculate Simpson's diversity, Gini-Simpson index, ENS, and evenness
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get_alpha_shannon() - Calculate Shannon's entropy, ENS, Pielou's evenness, and ENS-based evenness
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get_tip_index() - Get the index of a tip in a tree
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get_tip_edges() - Get the edges that lead to a tip
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file2gfm() - Decorate a file string for gfm markdown in Obsidian
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obs2gfm() - Decorate an Obsidian link for gfm markdown
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obs_callout() - Obsidian callout
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jak_theme() - Complete JAK theme
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jak_color() - Color defaults
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jak_grid() - Grid lines
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jak_legend() - Legend styling
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jak_strips() - Strip text styling
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jak_text() - Text sizes and styles
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jak_transparent() - Transparent backgrounds
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palette_jak() - A full-service color palette creator
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blend_palette() - Blend palette with a color
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scale_color_jak_d() - Custom discrete ggplot2 scale color
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scale_fill_jak_d() - Custom discrete ggplot2 scale fill
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get_color_palette() - Return table of colors for a palette
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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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get_luminance() - Title
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get_text_color() - Title
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seqtab_stats() - Extract DADA2 seqtab statistics
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seqtab_to_ft() - Make ft object from DADA2 seqtab
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ft - Feature table class
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get_asv_table - Return ASV table from ft object
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get_sequences - Return DNAstring object from ft object
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filter_asv_table - Filter an ft object by minimum count and sample
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cluster_asv_table - Cluster ASV sequences from ft object
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seqtab_stats_bind() - Stats of multiple seqtab objects
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seqtab_stats_plot() - Plot multiple seqtab objects
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card_parse() - Parse CARD database JSON file
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card_ab_info() - Get information about an antibiotic
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card_gene_info() - Get antibiotic information about a gene
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card_gene2ab() - Get gene information about an antibiotic
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card_ab2gene() - Get gene information about an antibiotic
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fastq_info_summary() - Summarize a fastq_info file
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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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get_package_info() - Package info utility
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get_session_info() - Session info utility
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jak_palettes - JAK color palettes
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jak_samp - Sample abundance matrix for examples and tests
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jak_tree - Sample phylogenetic tree for examples and tests
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EC_number_regex - Regular expression for EC numbers
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gene_symbol_regex - Regular expression for gene symbols