In ropensci/taxview: Tools for Vizualizing Data Taxonomically

taxview

knitr::opts_chunk$set(
  comment = "#>",
  collapse = TRUE,
  warning = FALSE
)

Summarise and visualize data sets taxonomically

The proposed workflow with taxview:

• input:
• data.frame with data, indicate which column has names or ids
• vector/list of names or ids (not associated with data)
• gather taxonomic classification data for each taxon
• from previously collected data, compute summary statistics/etc.
• visualize data among taxonomic groups, etc.

install

remotes::install_github("ropensci/taxview")

library(taxview)

use

get some data

x <- system.file("examples/plant_spp.csv", package = "taxview")

prepare data: clean, etc.

dat <- tibble::as_tibble(
 data.table::fread(x, stringsAsFactors = FALSE, 
   data.table = FALSE))
out <- tv_prep_ids(x, ids = dat$id, db = "ncbi")

Prepare summary. The output of tv_summarise() is an S3 class, with a summary of the groupings.

res <- tv_summarise(out)
res

The $summary slot has the number of taxa in the dataset

res$summary

The $by_rank slot has the breakdown of taxa within each rank category, as a count and percentage.

res$by_rank

The $by_rank_name slot has the breakdown of taxa ...

res$by_rank_name

The $by_within_rank slot has the breakdown of number of records within each taxon within each rank grouping.

res$by_within_rank[1:2]

visualize (NOT WORKING YET)

tv_viz(res)

Meta

• Please report any issues or bugs.
• License: MIT
• Get citation information for taxview in R doing citation(package = 'taxview')
• Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

ropensci/taxview documentation built on Sept. 13, 2022, 8:41 p.m.