Package index • jakR2

Genomics

read_orthogroups(): Import an orthofinder TSV file

orthogroup_list2counts(): Convert an orthogroup list dataframe to a count dataframe

Diversity

get_alpha_diversity(): Alpha-Diversity Measures

get_alpha_S(): Calculate richness (S) and sample depth

get_alpha_simpson(): Calculate Simpson's diversity index and its evenness and inverse

get_alpha_shannon(): Calculate Shannon's diversity index and its evenness and effective number of species (ENS)

Phlyogenetics

get_tip_index(): Get the index of a tip in a tree

get_tip_edges(): Get the edges that lead to a tip

Markdown

file2gfm(): Decorate a file string for gfm markdown in Obsidian

obs2gfm(): Decorate an Obsidian link for gfm markdown

Themes and Colors

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

get_color_palette(): Return table of colors for a palette

show_color_palette(): showColorPalette

show_all_color_palettes(): Show all color palettes in the jak_palettes object

get_luminance(): Title

get_text_color(): Title

Amplicons and ASVs

seqtab_stats(): Extract DADA2 seqtab statistics

seqtab_to_ft(): Make ft object from DADA2 seqtab

ft(): Feature table class

get_asv_table: Return ASV table from ft object

get_sequences: Return DNAstring object from ft object

filter_asv_table: Filter an ft object by minimum count and sample

cluster_asv_table: Cluster ASV sequences from ft object

CARD

card_parse(): Parse CARD database JSON file

card_ab_info(): Get information about an antibiotic

card_gene_info(): Get antibiotic information about a gene

card_gene2ab(): Get gene information about an antibiotic

card_ab2gene(): Get gene information about an antibiotic

fastq

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

Utilities

get_package_info(): Package info utility

get_session_info(): Session info utility