Package index
-
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 index and its evenness and inverse
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get_alpha_shannon()
- Calculate Shannon's diversity index and its evenness and effective number of species (ENS)
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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
-
file2gfm()
- Decorate a file string for gfm markdown in Obsidian
-
obs2gfm()
- Decorate an Obsidian link for gfm markdown
-
jak_theme()
- JAK ggplot theme
-
palette_jak()
- A full-service color palette creator
-
blend_palette()
- Blend palette with a color
-
scale_color_jak_d()
- Custom discrete ggplot2 scale color
-
scale_fill_jak_d()
- Custom discrete ggplot2 scale fill
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get_color_palette()
- Return table of colors for a palette
-
show_color_palette()
- showColorPalette
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show_all_color_palettes()
- Show all color palettes in the jak_palettes object
-
get_luminance()
- Title
-
get_text_color()
- Title
-
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
-
card_gene2ab()
- Get gene information about an antibiotic
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card_ab2gene()
- Get gene information about an antibiotic
-
fastq_info_summary()
- Summarize a fastq_info file
-
fastq_filter_summary_amplicon()
- Summarize a fastq_filter.py file in amplicon mode
-
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