metacoder: Tools for Parsing, Manipulating, and Graphing Hierarchical Data
Version 0.1.3

A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).

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AuthorZachary Foster [aut, cre], Niklaus Grunwald [ths]
Date of publication2017-05-23 05:36:48 UTC
MaintainerZachary Foster <zacharyfoster1989@gmail.com>
LicenseGPL-2 | GPL-3
Version0.1.3
URL https://grunwaldlab.github.io/metacoder_documentation/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("metacoder")

Man pages

add_alpha: add_alpha
apply_color_scale: Covert numbers to colors
arrange_obs: Sort columns of 'taxmap' objects
arrange_taxa: Sort columns of 'taxmap' objects
bryophytes_ex_data: Example dataset of bryophytes
can_be_num: Test if characters can be converted to numbers
check_element_length: Check length of graph attributes
class_from_class: Parse embedded classifications
class_from_name: Retrieve classifications from taxon names
class_from_obs_id: Retrieve classifications from observation IDs
class_from_taxon_id: Retrieve classifications from taxon IDs
class_to_taxonomy: List of classifications to taxonomy tree
contains: dplyr select_helpers
contaminants: Example dataset of contamination
convert_numeric_cols: Convert columns to numeric if appropriate
count_capture_groups: Count capture groups
delete_vetices_and_children: delete_vetices_and_children
diverging_palette: The default diverging color palette
DNAbin_to_char: Converts DNAbin to a named character vector
drawDetails.resizingTextGrob: Draws a resizingTextGrob
edge_list_depth: Get distance from root of edgelist observations
ends_with: dplyr select_helpers
everything: dplyr select_helpers
extract_taxonomy: Extract taxonomy information from sequence headers
fasta_headers: Get line numbers of FASTA headers
filter_obs: Filter observations with a list of conditions
filter_taxa: Filter taxa with a list of conditions
format_taxon_subset: Format taxon subset value
genbank_ex_data: Fungal ITS Genbank refseq
get_class_from_el: Get classification for taxa in edge list
get_edge_children: get_edge_children
get_edge_parents: get_edge_parents
get_id_from_name: Get taxon ID from name
get_name_from_id: Get taxon name from ID
get_node_children: get_node_children
get_numerics: Return numeric values in a character
get_optimal_range: Find optimal range
get_taxonomy_levels: Get taxonomy levels
grapes-greater-than-grapes: magrittr forward-pipe operator
heat_tree: Plot a taxonomic tree
hierarchies: Get classification of taxa
inter_circle_gap: Finds the gap/overlap of circle coordinates
inverse: Generate the inverse of a function
its1_ex_data: Example of ITS1 fungal data
label_bounds: Bounding box coords for labels
layout_functions: Layout functions
line_coords: Makes coordinates for a line
make_new_ids: Generate new unique IDs
make_plot_legend: Make color/size legend
make_text_grobs: Create a list of text grobs
map_unique: Run a function on unique values of a iterable
matches: dplyr select_helpers
metacoder: Metacoder
molten_dist: Get all distances between points
mutate_obs: Add columns to 'taxmap' objects
mutate_taxa: Add columns to 'taxmap' objects
ncbi_sequence: Downloads sequences from ids
ncbi_taxon_sample: Download representative sequences for a taxon
n_obs: Count observations in 'taxmap'
n_obs_1: Count observation assigned in 'taxmap'
n_subtaxa: Get number of subtaxa
n_subtaxa_1: Get number of subtaxa
n_supertaxa: Get number of supertaxa
num_range: dplyr select_helpers
obs: Get observations associated with taxa
obs_data: Return observation data from 'taxmap'
obs_data_colnames: Get column names of obs_data
obs_data_cols_used: Get names of obs_data in an unevaluated expression
one_of: dplyr select_helpers
parse_hmp_qiime: Parse HMP QIIME results
parse_mothur_summary: Parse mothur classification summary file
parse_primersearch: Parse EMBOSS primersearch output
parse_summary_seqs: Parse summary.seqs output
parse_taxonomy_table: Parse taxonomic data in a tsv/csv file
plot_alignment: Display sequence alignment
polygon_coords: Makes coordinates for a regualr polygon
postDrawDetails.resizingTextGrob: Clean up after the drawing.
pr2_ex_data: Example of PR2 SSU data
preDrawDetails.resizingTextGrob: Adjusts text size to viewport
primersearch: Use EMBOSS primersearch for in silico PCR
primersearch_is_installed: Test if primersearch is installed
print.taxmap: Print a 'taxmap' object
qualitative_palette: The default qualitative color palette
quantative_palette: The default quantative color palette
rdp_ex_data: Example of RDP Archea data
read_fasta: Read a FASTA file
read_lines_apply: Apply a function to chunks of a file
recursive_sample: Recursivly sample observations with a heirarchical...
remove_redundant_names: Remove the redundant taxon names
rename_duplicated: Number duplicated names
rescale: Rescale numeric vector to have specified minimum and maximum.
resizingTextGrob: Adds text grob that scales with viewport size
roots: Get root taxa
run_primersearch: Execute EMBOSS Primerseach
sample_frac_obs: Sample a proportion of observations from 'taxmap'
sample_frac_taxa: Sample a proportion of taxa from 'taxmap'
sample_n_obs: Sample n observations from 'taxmap'
sample_n_taxa: Sample n taxa from 'taxmap'
scale_bar_coords: Make scale bar division
select_labels: Pick labels to show
select_obs: Subset columns in a 'taxmap' object
select_taxa: Subset columns in a 'taxmap' object
silva_ex_data: Example dataset from SILVA
split_by_level: Splits a taxonomy at a specific level or rank
split_class_list: Split a list of classifications by a row/column value
starts_with: dplyr select_helpers
subtaxa: Get all subtaxa of a taxon
supertaxa: Get all supertaxa of a taxon
taxmap: Create an instance of 'taxmap'
taxon_data: Return taxon data from 'taxmap'
taxon_data_colnames: Get column names of taxon_data
taxon_data_cols_used: Get names of taxon_data in an unevaluated expression
taxonomic_sample: Recursivly sample a set of taxonomic assignments
taxonomy_ranks: Get ordered ranks from taxonomy
text_grob_length: Estimate text grob length
transform_data: Transformation functions
transmute_obs: Replace columns in 'taxmap' objects
transmute_taxa: Replace columns in 'taxmap' objects
unique_mapping: get indexes of a unique set of the input
unite_ex_data_1: Example of UNITE fungal ITS data
unite_ex_data_2: Example of UNITE fungal ITS data
unite_ex_data_3: Example of UNITE fungal ITS data
validate_regex_key_pair: Check a regex-key pair
validate_regex_match: Check that all match input
verify_color_range: Verify color range parameters
verify_label_count: Verify label count
verify_size: Verify size parameters
verify_size_range: Verify size range parameters
verify_trans: Verify transformation function parameters
vigilant_report: Report a error/warning if needed

Functions

DNAbin_to_char Man page Source code
\%>\% Man page
add_alpha Man page Source code
apply_color_scale Man page Source code
arrange_obs Man page Source code
arrange_taxa Man page Source code
bryophytes_ex_data Man page
can_be_num Man page Source code
check_element_length Man page Source code
class_from_class Man page Source code
class_from_name Man page Source code
class_from_obs_id Man page Source code
class_from_taxon_id Man page Source code
class_to_taxonomy Man page Source code
contains Man page
contaminants Man page
convert_numeric_cols Man page Source code
count_capture_groups Man page Source code
delete_vetices_and_children Man page Source code
diverging_palette Man page Source code
drawDetails.resizingTextGrob Man page Source code
edge_list_depth Man page Source code
ends_with Man page
everything Man page
extract_taxonomy Man page Source code
extract_taxonomy.DNAbin Man page Source code
extract_taxonomy.default Man page Source code
extract_taxonomy.list Man page Source code
fasta_headers Man page Source code
filter_obs Man page Source code
filter_taxa Man page Source code
format_taxon_subset Man page Source code
genbank_ex_data Man page
get_class_from_el Man page Source code
get_edge_children Man page Source code
get_edge_parents Man page Source code
get_id_from_name Man page Source code
get_name_from_id Man page Source code
get_node_children Man page Source code
get_numerics Man page Source code
get_optimal_range Man page Source code
get_taxonomy_levels Man page Source code
heat_tree Man page Source code
heat_tree.default Man page Source code
heat_tree.taxmap Man page Source code
hierarchies Man page Source code
inter_circle_gap Man page Source code
inverse Man page Source code
its1_ex_data Man page
label_bounds Man page Source code
layout_functions Man page Source code
line_coords Man page Source code
make_new_ids Man page Source code
make_plot_legend Man page Source code
make_text_grobs Man page Source code
map_unique Man page Source code
matches Man page
metacoder Man page
metacoder-package Man page
molten_dist Man page Source code
mutate_obs Man page Source code
mutate_taxa Man page Source code
n_obs Man page Source code
n_obs_1 Man page Source code
n_subtaxa Man page Source code
n_subtaxa_1 Man page Source code
n_supertaxa Man page Source code
ncbi_sequence Man page Source code
ncbi_taxon_sample Man page Source code
num_range Man page
obs Man page Source code
obs_data Man page Source code
obs_data_colnames Man page Source code
obs_data_cols_used Man page Source code
one_of Man page
parse_hmp_qiime Man page Source code
parse_mothur_summary Man page Source code
parse_primersearch Man page Source code
parse_summary_seqs Man page Source code
parse_taxonomy_table Man page Source code
plot_alignment Man page Source code
polygon_coords Man page Source code
postDrawDetails.resizingTextGrob Man page Source code
pr2_ex_data Man page
preDrawDetails.resizingTextGrob Man page Source code
primersearch Man page Source code
primersearch.character Man page Source code
primersearch.taxmap Man page Source code
primersearch_is_installed Man page Source code
print.taxmap Man page Source code
qualitative_palette Man page Source code
quantative_palette Man page Source code
rdp_ex_data Man page
read_fasta Man page Source code
read_lines_apply Man page Source code
recursive_sample Man page Source code
remove_redundant_names Man page Source code
rename_duplicated Man page Source code
rescale Man page Source code
resizingTextGrob Man page Source code
roots Man page Source code
run_primersearch Man page Source code
sample_frac_obs Man page Source code
sample_frac_taxa Man page Source code
sample_n_obs Man page Source code
sample_n_taxa Man page Source code
scale_bar_coords Man page Source code
select_labels Man page Source code
select_obs Man page Source code
select_taxa Man page Source code
silva_ex_data Man page
split_by_level Man page Source code
split_class_list Man page Source code
starts_with Man page
subtaxa Man page Source code
supertaxa Man page Source code
taxmap Man page Source code
taxon_data Man page Source code
taxon_data_colnames Man page Source code
taxon_data_cols_used Man page Source code
taxonomic_sample Man page Source code
taxonomy_ranks Man page Source code
text_grob_length Man page Source code
transform_data Man page Source code
transmute_obs Man page Source code
transmute_taxa Man page Source code
unique_mapping Man page Source code
unite_ex_data_1 Man page
unite_ex_data_2 Man page
unite_ex_data_3 Man page
validate_regex_key_pair Man page Source code
validate_regex_match Man page Source code
verify_color_range Man page Source code
verify_label_count Man page Source code
verify_size Man page Source code
verify_size_range Man page Source code
verify_trans Man page Source code
vigilant_report Man page Source code

Files

inst
inst/CITATION
inst/extdata
inst/extdata/unite_general_release.fasta
inst/extdata/silva_nr99.fasta
inst/extdata/pr2_stramenopiles_gb203.fasta
inst/extdata/mothur_16S_training_subset.fasta.gz
inst/extdata/rdp_current_Archaea_unaligned.fa
inst/extdata/ncbi_basidiomycetes.fasta
inst/extdata/its1_chytridiomycota_hmm.fasta
inst/doc
inst/doc/introduction.R
inst/doc/introduction.html
inst/doc/introduction.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/Rplots.pdf
tests/testthat/test--taxmap--arrange.R
tests/testthat/test--heat_tree.R
tests/testthat/test--taxmap--mutate.R
tests/testthat/test--taxmap--sample.R
tests/testthat/test--taxmap--select.R
tests/testthat/test--taxmap--utilities.R
tests/testthat/test--taxmap.R
tests/testthat/test--taxmap--filter.R
tests/testthat/test--extract_taxonomy.R
NAMESPACE
NEWS.md
data
data/genbank_ex_data.rda
data/silva_ex_data.rda
data/unite_ex_data_2.rda
data/its1_ex_data.rda
data/pr2_ex_data.rda
data/bryophytes_ex_data.rda
data/unite_ex_data_1.rda
data/contaminants.rda
data/unite_ex_data_3.rda
data/rdp_ex_data.rda
R
R/taxmap--class.R
R/heat_tree.R
R/taxmap--utilities.R
R/extract_taxonomy--internal.R
R/heat_tree--vertex_size.R
R/sequence_download.R
R/taxmap--mutate.R
R/mothur.R
R/in_silico_pcr.R
R/taxmap--sample.R
R/taxmap--column_generators.R
R/metacoder-package.r
R/taxmap--internal.R
R/heat_tree--shape_generators.R
R/old_code.R
R/dataset_documentation.R
R/heat_tree--resizing_text.R
R/taxmap--arrange.R
R/reading_files.R
R/taxonomy.R
R/taxonomic_sample.R
R/taxmap--select.R
R/internal.R
R/heat_tree--internal.R
R/extract_taxonomy--wrappers.R
R/heat_tree--layouts.R
R/plot_alignment.R
R/extract_taxonomy.R
R/heat_tree--mapping.R
R/taxmap--filter.R
R/extract_taxonomy--parsers.R
R/heat_tree--legend.R
R/imports.R
vignettes
vignettes/introduction.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/polygon_coords.Rd
man/diverging_palette.Rd
man/get_numerics.Rd
man/taxmap.Rd
man/validate_regex_match.Rd
man/grapes-greater-than-grapes.Rd
man/starts_with.Rd
man/get_node_children.Rd
man/can_be_num.Rd
man/mutate_obs.Rd
man/unite_ex_data_2.Rd
man/drawDetails.resizingTextGrob.Rd
man/filter_taxa.Rd
man/one_of.Rd
man/molten_dist.Rd
man/verify_label_count.Rd
man/line_coords.Rd
man/ends_with.Rd
man/unite_ex_data_1.Rd
man/run_primersearch.Rd
man/sample_n_taxa.Rd
man/print.taxmap.Rd
man/select_obs.Rd
man/taxon_data.Rd
man/get_class_from_el.Rd
man/get_edge_children.Rd
man/format_taxon_subset.Rd
man/rdp_ex_data.Rd
man/n_subtaxa.Rd
man/DNAbin_to_char.Rd
man/inverse.Rd
man/vigilant_report.Rd
man/n_supertaxa.Rd
man/its1_ex_data.Rd
man/get_id_from_name.Rd
man/fasta_headers.Rd
man/layout_functions.Rd
man/transform_data.Rd
man/plot_alignment.Rd
man/transmute_obs.Rd
man/count_capture_groups.Rd
man/text_grob_length.Rd
man/num_range.Rd
man/arrange_obs.Rd
man/n_obs_1.Rd
man/ncbi_taxon_sample.Rd
man/convert_numeric_cols.Rd
man/extract_taxonomy.Rd
man/qualitative_palette.Rd
man/delete_vetices_and_children.Rd
man/unique_mapping.Rd
man/preDrawDetails.resizingTextGrob.Rd
man/quantative_palette.Rd
man/edge_list_depth.Rd
man/label_bounds.Rd
man/resizingTextGrob.Rd
man/parse_summary_seqs.Rd
man/scale_bar_coords.Rd
man/parse_taxonomy_table.Rd
man/get_name_from_id.Rd
man/matches.Rd
man/make_plot_legend.Rd
man/filter_obs.Rd
man/get_taxonomy_levels.Rd
man/split_class_list.Rd
man/read_fasta.Rd
man/parse_hmp_qiime.Rd
man/bryophytes_ex_data.Rd
man/recursive_sample.Rd
man/sample_frac_taxa.Rd
man/get_optimal_range.Rd
man/n_obs.Rd
man/select_labels.Rd
man/primersearch_is_installed.Rd
man/arrange_taxa.Rd
man/inter_circle_gap.Rd
man/parse_primersearch.Rd
man/sample_frac_obs.Rd
man/check_element_length.Rd
man/select_taxa.Rd
man/apply_color_scale.Rd
man/validate_regex_key_pair.Rd
man/remove_redundant_names.Rd
man/obs_data_cols_used.Rd
man/rescale.Rd
man/hierarchies.Rd
man/add_alpha.Rd
man/pr2_ex_data.Rd
man/genbank_ex_data.Rd
man/silva_ex_data.Rd
man/read_lines_apply.Rd
man/transmute_taxa.Rd
man/supertaxa.Rd
man/taxon_data_colnames.Rd
man/verify_color_range.Rd
man/n_subtaxa_1.Rd
man/metacoder.Rd
man/parse_mothur_summary.Rd
man/mutate_taxa.Rd
man/contains.Rd
man/verify_size_range.Rd
man/postDrawDetails.resizingTextGrob.Rd
man/taxonomy_ranks.Rd
man/taxonomic_sample.Rd
man/primersearch.Rd
man/rename_duplicated.Rd
man/make_text_grobs.Rd
man/class_from_name.Rd
man/subtaxa.Rd
man/class_from_taxon_id.Rd
man/get_edge_parents.Rd
man/obs_data.Rd
man/heat_tree.Rd
man/sample_n_obs.Rd
man/unite_ex_data_3.Rd
man/map_unique.Rd
man/contaminants.Rd
man/make_new_ids.Rd
man/class_to_taxonomy.Rd
man/roots.Rd
man/everything.Rd
man/verify_size.Rd
man/obs_data_colnames.Rd
man/taxon_data_cols_used.Rd
man/class_from_obs_id.Rd
man/ncbi_sequence.Rd
man/obs.Rd
man/class_from_class.Rd
man/verify_trans.Rd
man/split_by_level.Rd
metacoder documentation built on May 23, 2017, 9:10 a.m.