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

ambiguous_patternsGet patterns for ambiguous taxa
ambiguous_synonymsGet patterns for ambiguous taxa
apply_color_scaleCovert numbers to colors
as_phyloseqConvert taxmap to phyloseq
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
check_element_lengthCheck length of graph attributes
check_for_pkgcheck for packages
check_option_groupsCheck option: groups
compare_groupsCompare groups of samples
complementFind complement of sequences
containsdplyr select_helpers
convert_baseConverts decimal numbers to other bases
counts_to_presenceApply a function to groups of columns
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
everythingdplyr select_helpers
fasta_headersGet line numbers of FASTA headers
filter_ambiguous_taxaFilter ambiguous taxon names
get_class_from_elGet classification for taxa in edge 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_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
hmp_otusA HMP subset
hmp_samplesSample information for HMP subset
inter_circle_gapFinds the gap/overlap of circle coordinates
inverseGenerate the inverse of a function
is_ambiguousFind ambiguous taxon names
label_boundsBounding box coords for labels
layout_functionsLayout functions
limited_printPrint a subset of a character vector
line_coordsMakes coordinates for a line
look_for_naLook for NAs in parameters
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_uniqueRun a function on unique values of a iterable
matchesdplyr select_helpers
molten_distGet all distances between points
my_printPrint something
ncbi_sequenceDownloads sequences from ids
ncbi_taxon_sampleDownload representative sequences for a taxon
num_rangedplyr select_helpers
one_ofdplyr select_helpers
parse_dada2Convert the output of dada2 to a taxmap object
parse_edge_listConvert a table with an edge list to taxmap
parse_greengenesParse Greengenes release
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_primersearchParse EMBOSS primersearch output
parse_qiime_biomParse a BIOM output from QIIME
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_ubiomeConverts the uBiome file format to taxmap
parse_unite_generalParse UNITE general release FASTA
polygon_coordsMakes coordinates for a regular polygon
primersearchUse EMBOSS primersearch for in silico PCR
primersearch_is_installedTest if primersearch is installed
primersearch_rawUse EMBOSS primersearch for in silico PCR
qualitative_paletteThe default qualitative color palette
quantative_paletteThe default quantative color palette
rarefy_obsCalculate rarefied observation counts
read_fastaRead a FASTA file
read_lines_applyApply a function to chunks of a file
repo_urlReturn github url
rescaleRescale numeric vector to have specified minimum and maximum.
rev_compRevere complement sequences
reverseReverse sequences
run_primersearchExecute EMBOSS Primersearch
scale_bar_coordsMake scale bar division
select_labelsPick labels to show
split_by_levelSplits a taxonomy at a specific level or rank
starts_withdplyr select_helpers
startup_msgReturn startup message
text_grob_lengthEstimate text grob length
transform_dataTransformation functions
unique_mappingget indexes of a unique set of the input
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 April 30, 2020, 1:06 a.m.