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

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

Author
Zachary Foster [aut, cre], Niklaus Grunwald [ths]
Date of publication
2016-08-27 00:35:09
Maintainer
Zachary Foster <zacharyfoster1989@gmail.com>
License
GPL-2 | GPL-3
Version
0.1.2

View on CRAN

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
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 comtamination
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 defualt 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_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
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 beween 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 defualt qualitative color palette
quantative_palette
The defualt 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

Files in this package

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