Summarise and visualize data sets wrt taxonomy
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README.md

taxview

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. Build Status

Summarise and visualize data sets from with respect to taxonomy

install

devtools::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))
head(dat)
## # A tibble: 6 x 2
##                     name      id
##                    <chr>   <int>
## 1       Dianthus engleri 1531994
## 2   Anacolosa frutescens 1618138
## 3 Hymenophyllum plicatum  638568
## 4       Dolichos oliveri 1094718
## 5      Kalanchoe montana  441235
## 6      Caladenia plicata  672428
dat_clean <- tv_clean_ids(x, ids = dat$id, db = "ncbi")
head(dat_clean)
##                 name         rank     id   query
## 1 cellular organisms      no rank 131567 1531994
## 2          Eukaryota superkingdom   2759 1531994
## 3      Viridiplantae      kingdom  33090 1531994
## 4       Streptophyta       phylum  35493 1531994
## 5     Streptophytina    subphylum 131221 1531994
## 6        Embryophyta      no rank   3193 1531994

prepare summary

(sumdat <- tv_summarise(dat_clean))
<tv_summary>
 no. taxa: 129
 by rank: N (21)
 by rank name: N (594)
 within ranks: N (20)

visualize (NOT WORKING YET)

tv_viz(sumdat)

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for taxview in R doing citation(package = 'taxview')
  • 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.