Sort columns of taxmap
objects Retrieve classifications from taxon names
Parse embedded classifications
Example dataset of bryophytes
add_alpha
Sort columns of taxmap
objects Covert numbers to colors
Retrieve classifications from taxon IDs
Retrieve classifications from observation IDs
Check length of graph attributes
The defualt diverging color palette
Converts DNAbin to a named character vector
Example dataset of comtamination
Get distance from root of edgelist observations
delete_vetices_and_children
delete_vetices_and_children
Convert columns to numeric if appropriate
Count capture groups
drawDetails.resizingTextGrob
Draws a resizingTextGrob
List of classifications to taxonomy tree
dplyr select_helpers
get_edge_children
Extract taxonomy information from sequence headers
dplyr select_helpers
Format taxon subset value
Fungal ITS Genbank refseq
Get classification for taxa in edge list
get_edge_parents
dplyr select_helpers
Get taxon ID from name
Get line numbers of FASTA headers
Get taxon name from ID
Get classification of taxa
get_node_children
Get taxonomy levels
Find optimal range
magrittr forward-pipe operator
Plot a taxonomic tree
Finds the gap/overlap of circle coordinates
Example of ITS1 fungal data
Generate the inverse of a function
Get all distances beween points
Add columns to taxmap
objects dplyr select_helpers
Metacoder
Create a list of text grobs
Make color/size legend
Generate new unique IDs
Run a function on unique values of a iterable
Layout functions
Makes coordinates for a line
dplyr select_helpers
Get column names of obs_data
Parse EMBOSS primersearch output
Get number of subtaxa
Count observations in taxmap
Parse summary.seqs output
The defualt quantative color palette
Read a FASTA file
Example of RDP Archea data
Apply a function to chunks of a file
Splits a taxonomy at a specific level or rank
Add columns to taxmap
objects Split a list of classifications by a row/column value
Parse taxonomic data in a tsv/csv file
Count observation assigned in taxmap
Display sequence alignment
postDrawDetails.resizingTextGrob
Clean up after the drawing.
Makes coordinates for a regualr polygon
Execute EMBOSS Primerseach
Sample a proportion of observations from taxmap
Sample n taxa from taxmap
Get names of obs_data in an unevaluated expression
Use EMBOSS primersearch for in silico PCR
Return observation data from taxmap
primersearch_is_installed
Test if primersearch is installed
Get root taxa
Adds text grob that scales with viewport size
Get all subtaxa of a taxon
dplyr select_helpers
Get column names of taxon_data
Recursivly sample observations with a heirarchical classification
Remove the redundant taxon names
Recursivly sample a set of taxonomic assignments
Return taxon data from taxmap
Verify color range parameters
Check that all match input
Downloads sequences from ids
Download representative sequences for a taxon
Parse HMP QIIME results
Parse mothur classification summary file
Example of PR2 SSU data
preDrawDetails.resizingTextGrob
Adjusts text size to viewport
Rescale numeric vector to have specified minimum and maximum.
Number duplicated names
Example dataset from SILVA
Pick labels to show
Get observations associated with taxa
Get number of subtaxa
dplyr select_helpers
Get number of supertaxa
The defualt qualitative color palette
Sample n observations from taxmap
Sample a proportion of taxa from taxmap
Replace columns in taxmap
objects Transformation functions
Get names of taxon_data in an unevaluated expression
Example of UNITE fungal ITS data
Example of UNITE fungal ITS data
Make scale bar division
Estimate text grob length
Get ordered ranks from taxonomy
Verify label count
Verify size range parameters
Verify transformation function parameters
Verify size parameters
Replace columns in taxmap
objects get indexes of a unique set of the input
Report a error/warning if needed
Get all supertaxa of a taxon
Create an instance of taxmap
Example of UNITE fungal ITS data
Check a regex-key pair