This software provides programmatic access to the Chromosome Counts Database ( CCDB ) API. The CCDB is a residential district resource for plant chromosome numbers. For more details on the database, see the associated publication by Rice et alabama. in New Phytologist .
This package is maintained by Paula Andrea Martinez and once maintained by Matthew Pennell who are not affiliated with the CCDB group. The URL for Chromer department of commerce is hypertext transfer protocol : //docs.ropensci.org/chromer/.
The software can be installed directly from CRAN, but it is presently outdated — PLEASE install directly from GitHub
or, for the latest version, you can install immediately from GitHub using devtools
## install.packages ( `` devtools '' ) devtools : :install_github(
Querying the CCDB
It is possible to query the database in three ways : by
majorGroup. For example, if we are concerned in the genus Solanum ( Solanaceae ), which contains the potato, tomato, and eggplant, we would query the database as follows
library( chromer) sol_gen < - chrom_counts( taxonomic group =
", crying =
") head( sol_gen) nrow( sol_gen)
There are over 3000 records for Solanum alone ! If we are interest in a particular species, such as tomatoes, we can search for the species directly .
sol_tom < - chrom_counts( taxonomic group =
", crying =
") head( sol_tom)
taxa="Solanum lycopersicum" ( including a space between the genus and species name ) will besides work here .
If we wanted to get data on the solid family, we simply type
", rate =
") head( sol_fam)
Or, expand the setting much further and get all Angiosperms ( this will take some time )
air national guard < - chrom_counts( taxonomic group =
", rank =
") head( air national guard)
There are two options for returning data. The first ( nonpayment ) is to only return the species appoint information ( including taxonomic resolutions made by Taxonome ) and the haploid and diploid counts. Setting the argument
sol_gen_full < - chrom_counts(
", rank =
", full = true)
returns a bunch more information on the records .
Summarizing the data
The Chromosome Counts Database is a fantastic resource but as it is a compilation of a large total of resources and studies, the datum is slightly messy and challenging to work with. We have written a short function that does some post-processing to make it easier to handle. The function
summarize_counts() does the follow :
- Aggregates multiple records for the like species
- Infers the gametophytic ( haploid ) number of chromosomes when only the sporophytic ( diploid ) counts are available.
- Parses the records for numeric values. In some cases chromosomal counts besides include textbook characters ( for example, # – # ; c. # ; #, #, # ; and many other varieties ). As there are many possible ways that chromosomal counts may be listed in the database, the officiate takes the uninstructed access and just searches the strings for integers. In most cases, this is reasonable but may produces weird results on juncture. Some degree of manual curation will probably be necessary and the output of the summary should be used with caution in downstream analyses .
To summarize and clean the count data obtained from
chrom_counts() just use
- Please report any issues or bugs.
- License: CC0
- Get citation information for
chromerin R doing
citation(package = "chromer")
- Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.