Man pages for metacoder
Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

all_functionsGet list of usable functions
all_namesReturn names of data in [taxonomy()] or [taxmap()]
ambiguous_patternsGet patterns for ambiguous taxa
ambiguous_synonymsGet patterns for ambiguous taxa
apply_color_scaleCovert numbers to colors
arrange_obsSort user data in [taxmap()] objects
arrange_taxaSort the edge list of [taxmap()] objects
as_idConvert a vector to database IDs
as_phyloseqConvert taxmap to phyloseq
branchesGet "branch" taxa
calc_group_meanCalculate means of groups of columns
calc_group_medianCalculate medians of groups of columns
calc_group_rsdRelative standard deviations of groups of columns
calc_group_statApply a function to groups of columns
calc_n_samplesCount the number of samples
calc_obs_propsCalculate proportions from observation counts
calc_prop_samplesCalculate the proportion of samples
calc_taxon_abundSum observation values for each taxon
can_be_numTest if characters can be converted to numbers
can_be_used_in_taxmapCheck that a unknown object can be used with taxmap
check_class_colCheck for name/index in input data
check_element_lengthCheck length of graph attributes
check_for_pkgcheck for packages
check_option_groupsCheck option: groups
check_taxmap_dataCheck dataset format
classificationsGet classifications of taxa
compare_groupsCompare groups of samples
complementFind complement of sequences
containsdplyr select_helpers
convert_baseConverts decimal numbers to other bases
correct_taxon_namesLook up official names from potentially misspelled names
count_capture_groupsCount capture groups
counts_to_presenceApply a function to groups of columns
database_listDatabase list
data_usedGet values of data used in expressions
desc_fontDescription formatting in print methods
diverging_paletteThe default diverging color palette
DNAbin_to_charConverts DNAbin to a named character vector
do_calc_on_num_colsRun some function to produce new columns.
dot-onAttachRun when package loads
edge_list_depthGet distance from root of edgelist observations
ends_withdplyr select_helpers
error_fontFont to indicate an error
everythingdplyr select_helpers
ex_hierarchiesAn example hierarchies object
ex_hierarchy1An example Hierarchy object
ex_hierarchy2An example Hierarchy object
ex_hierarchy3An example Hierarchy object
ex_taxmapAn example taxmap object
extract_tax_dataExtracts taxonomy info from vectors with regex
fasta_headersGet line numbers of FASTA headers
filter_ambiguous_taxaFilter ambiguous taxon names
filtering-helpersTaxonomic filtering helpers
filter_obsFilter observations with a list of conditions
filter_taxaFilter taxa with a list of conditions
get_class_from_elGet classification for taxa in edge list
get_dataGet data in a taxmap object by name
get_database_nameReturn name of database
get_data_frameGet data in a taxonomy or taxmap object by name
get_datasetGet a data set from a taxmap object
get_dots_or_listGet input from dots or list
get_expected_dataGet a data set in as_phyloseq
get_numeric_colsGet numeric columns from taxmap table
get_numericsReturn numeric values in a character
get_optimal_rangeFind optimal range
get_sort_varGet a vector from a vector/list/table to be used in mapping
get_taxmap_colsGet a column subset
get_taxmap_dataGet a data set from a taxmap object
get_taxmap_other_colsParse the other_cols option
get_taxmap_tableGet a table from a taxmap object
get_taxonomy_levelsGet taxonomy levels
grapes-greater-than-grapesmagrittr forward-pipe operator
heat_treePlot a taxonomic tree
heat_tree_matrixPlot a matrix of heat trees
hierarchiesMake a set of many [hierarchy()] class objects
hierarchyThe Hierarchy class
highlight_taxon_idsHighlight taxon ID column
hmp_otusA HMP subset
hmp_samplesSample information for HMP subset
id_classificationsGet ID classifications of taxa
init_taxmap_dataConvert 'data' input for Taxamp
inter_circle_gapFinds the gap/overlap of circle coordinates
internodesGet "internode" taxa
inverseGenerate the inverse of a function
is_ambiguousFind ambiguous taxon names
is_branchTest if taxa are branches
is_internodeTest if taxa are "internodes"
is_leafTest if taxa are leaves
is_rootTest if taxa are roots
is_stemTest if taxa are stems
label_boundsBounding box coords for labels
layout_functionsLayout functions
leavesGet leaf taxa
leaves_applyApply function to leaves of each taxon
length_of_thingCheck length of thing
limited_printPrint a subset of a character vector
line_coordsMakes coordinates for a line
look_for_naLook for NAs in parameters
lookup_tax_dataConvert one or more data sets to taxmap
make_dada2_asv_tableMake a imitation of the dada2 ASV abundance matrix
make_dada2_tax_tableMake a imitation of the dada2 taxonomy matrix
make_fasta_with_u_replacedMake a temporary file U's replaced with T
make_plot_legendMake color/size legend
map_dataCreate a mapping between two variables
map_data_Create a mapping without NSE
map_uniqueRun a function on unique values of a iterable
matchesdplyr select_helpers
molten_distGet all distances between points
multi_sep_splitLike 'strsplit', but with multiple separators
mutate_obsAdd columns to [taxmap()] objects
my_printPrint something
name_fontVariable name formatting in print methods
names_usedGet names of data used in expressions
ncbi_sequenceDownloads sequences from ids
ncbi_taxon_sampleDownload representative sequences for a taxon
n_leavesGet number of leaves
n_leaves_1Get number of leaves
n_obsCount observations in [taxmap()]
n_obs_1Count observation assigned in [taxmap()]
n_subtaxaGet number of subtaxa
n_subtaxa_1Get number of subtaxa
n_supertaxaGet number of supertaxa
n_supertaxa_1Get number of supertaxa
num_rangedplyr select_helpers
obsGet data indexes associated with taxa
obs_applyApply function to observations per taxon
one_ofdplyr select_helpers
parse_dada2Convert the output of dada2 to a taxmap object
parse_datasetParse options specifying datasets
parse_edge_listConvert a table with an edge list to taxmap
parse_greengenesParse Greengenes release
parse_heirarchies_to_taxonomyInfer edge list from hierarchies
parse_mothur_taxonomyParse mothur Classify.seqs *.taxonomy output
parse_mothur_tax_summaryParse mothur *.tax.summary Classify.seqs output
parse_newickParse a Newick file
parse_phyloParse a phylo object
parse_phyloseqConvert a phyloseq to taxmap
parse_possibly_named_logicalused to parse inputs to 'drop_obs' and 'reassign_obs'
parse_primersearchParse EMBOSS primersearch output
parse_qiime_biomParse a BIOM output from QIIME
parse_raw_heirarchies_to_taxonomyInfer edge list from hierarchies composed of character...
parse_rdpParse RDP FASTA release
parse_seq_inputRead sequences in an unknown format
parse_silva_fastaParse SILVA FASTA release
parse_summary_seqsParse summary.seqs output
parse_tax_dataConvert one or more data sets to taxmap
parse_ubiomeConverts the uBiome file format to taxmap
parse_unite_generalParse UNITE general release FASTA
polygon_coordsMakes coordinates for a regular polygon
prefixed_printPrint a object with a prefix
primersearchUse EMBOSS primersearch for in silico PCR
primersearch_is_installedTest if primersearch is installed
primersearch_rawUse EMBOSS primersearch for in silico PCR
print__characterPrint a character
print__data.framePrint a data.frame
print__default_Print method for unsupported
print__factorPrint a factor
print__integerPrint an integer
print_itemPrint a item
print__listPrint a list
print__logicalPrint a logical
print__matrixPrint a matrix
print__numericPrint a numeric
print__orderedPrint a ordered factor
print__tbl_dfPrint a tibble
print_treePrint a text tree
print__vectorGeneric vector printer
progress_lapplylappy with progress bars
punc_fontPunctuation formatting in print methods
qualitative_paletteThe default qualitative color palette
quantative_paletteThe default quantative color palette
ranks_refLookup-table for IDs of taxonomic ranks
rarefy_obsCalculate rarefied observation counts
read_fastaRead a FASTA file
read_lines_applyApply a function to chunks of a file
remove_redundant_namesRemove redundant parts of taxon names
replace_taxon_idsReplace taxon ids
repo_urlReturn github url
rescaleRescale numeric vector to have specified minimum and maximum.
rev_compRevere complement sequences
reverseReverse sequences
rootsGet root taxa
run_primersearchExecute EMBOSS Primersearch
sample_frac_obsSample a proportion of observations from [taxmap()]
sample_frac_taxaSample a proportion of taxa from [taxonomy()] or [taxmap()]
sample_n_obsSample n observations from [taxmap()]
sample_n_taxaSample n taxa from [taxonomy()] or [taxmap()]
scale_bar_coordsMake scale bar division
select_labelsPick labels to show
select_obsSubset columns in a [taxmap()] object
simplifyList to vector of unique elements
split_by_levelSplits a taxonomy at a specific level or rank
starts_withdplyr select_helpers
startup_msgReturn startup message
stemsGet stem taxa
subtaxaGet subtaxa
subtaxa_applyApply function to subtaxa of each taxon
supertaxaGet all supertaxa of a taxon
supertaxa_applyApply function to supertaxa of each taxon
taxaA class for multiple taxon objects
taxmapTaxmap class
taxonTaxon class
taxon_databaseTaxonomy database class
taxon_idTaxon ID class
taxon_idsGet taxon IDs
taxon_indexesGet taxon indexes
taxon_nameTaxon name class
taxon_namesGet taxon names
taxonomyTaxonomy class
taxonomy_tableConvert taxonomy info to a table
taxon_rankTaxon rank class
taxon_ranksGet taxon ranks
text_grob_lengthEstimate text grob length
tid_fontTaxon id formatting in print methods
to_percentFormat a proportion as a printed percent
transform_dataTransformation functions
transmute_obsReplace columns in [taxmap()] objects
unique_mappingget indexes of a unique set of the input
validate_regex_key_pairCheck a regex-key pair
validate_regex_matchCheck that all match input
validate_taxmap_funcsValidate 'funcs' input for Taxamp
verify_color_rangeVerify color range parameters
verify_label_countVerify label count
verify_sizeVerify size parameters
verify_size_rangeVerify size range parameters
verify_taxmapCheck that an object is a taxmap
verify_transVerify transformation function parameters
write_greengenesWrite an imitation of the Greengenes database
write_mothur_taxonomyWrite an imitation of the Mothur taxonomy file
write_rdpWrite an imitation of the RDP FASTA database
write_silva_fastaWrite an imitation of the SILVA FASTA database
write_unite_generalWrite an imitation of the UNITE general FASTA database
zero_low_countsReplace low counts with zero
metacoder documentation built on June 24, 2021, 1:07 a.m.