Package index • bubbler

All functions

add_other(): Add an "Other" observation to a relative abundance table.

add_unclassified(): Add an "Unclassified" observation to a relative abundance table.

all_taxa(): Return a character vector of unique taxa from a relative abundance table.

arrange_sample_by_taxa(): Arrange samples by the most abundant taxa.

arrange_taxa(): Arrange taxa by abundance.

arrange_var(): Arrange a variable by the ordering of another variable

arrange_var_abund(): Arrange a variable by its grouped relative abundance

asv_data_phy(): Grab asv table from a physeq object and format to tibble

asv_data_qiime(): Grab asv table from a .qza file and format to tibble.

asv_data_tsv(): Grab asv table from a tsv file and format to tibble

asv_tree(): Generate a ggtree object based on the distance metric, from asv data

bar_plot(): Generate a ggplot2 stacked barplot from a relative abundance table.

bubble_plot(): Generate a ggplot2 bubble plot

choose_n_taxa(): Choose how many taxa to display when plotting

combine_dataframes(): Combine data.frames that are in a list.

detect_threshold(): Detect the label used for threshold from a pooled relative_abundance table

detect_threshold_vec(): Detect the label used in a character vector.

extract_unique_taxa(): Get the unique taxa from the combined data.frame.

global_colour_scheme(): Set a global colour scheme for a series of plots.

is_q2metadata(): checks if metadata is in qiime2 (.tsv)

meta_data_phy(): Grab metadata from a physeq object and format to tibble

meta_data_qiime(): Grab metadata table from a .tsv QIIME2-formatted file and format to tibble.

meta_data_tsv(): Grab metadata table from a tsv file and format to tibble

physeq: Phyloseq object for bubbler

pool_taxa(): Pool taxa according to threshold

read_bracken_file(): Grab bracken data and format to tibble.

read_q2biom(): read qiime2 biom file (version 2.1)

read_q2metadata(): read qiime2 metadata (.tsv)

read_qza(): read qiime2 artifacts (.qza)

rel_abund_bracken(): Generate a relative abundance table using kracken2/bracken data.

rel_abund_phy(): Generate a relative abundance table in tibble format from a phyloseq object.

rel_abund_qiime(): Generate a relative abundance table in tibble form, from QIIME2 artifacts.

rel_abund_tsv(): Generate a relative abundance table in tibble format from tsv files.

show_top_taxa(): Show the top taxa of a rel_abund table

subset_high_low(): Subset the highest or lowest abundance samples from a relative abundance table.

subset_rel_abund(): Subset samples from a relative abundance table.

sum_rel_abund(): Sum the relative abundance across variables.

taxa_data_phy(): Grab taxa table from a physeq object and format to tibble

taxa_data_qiime(): Grab taxonomy table from a .qza file and format to tibble.

taxa_data_tsv(): Grab taxa table from a tsv file and format to tibble

taxon_italics(): Convert taxon to italics, ignoring threshold, from a relative abundance tibble.

tip_order(): Grab the order of tips (sample_id) to use as levels for plotting.