DiatoViz is an R package developed for diatomists.
The DiatoViz package provides a simple function to add silhouettes of
diatoms to plots generated ggplot2. Currently, the package contains 89
diatom silhouettes. The silhouettes of diatoms were created using the
SHERPA software (Kloster
et al. 2014).
You can install the development version of DiatoViz from
GitHub with R package
remotes:
#install.packages("remotes")
remotes::install_github("junqueiragaabi/DiatoViz")To use Diatoviz, your species list must be formatted with the specific
abbreviations provided by the Omnidia
software. The main function geom_diatom_code() geometry draws diatom
species shapes. Here you can see some the current available diatoms to
plot.
library(tidyverse)
library(DiatoViz)
diatoms <- DiatoViz::valid_diatom_code()
df_example <- data.frame(
a = c(rep(1:5, 17),c(1,2,3,4)),
b = sort(c(rep(1:17, 5), c(0,0,0,0)), decreasing = TRUE),
species = diatoms) %>%
slice(1:30)
ggplot(df_example, aes(x = a, y = b)) +
geom_diatom_code(aes(diatom_code = species), height = 0.1) +
geom_label(aes(label = species), nudge_y = -0.45) +
theme_void()+
theme(plot.margin = margin(15,15,15,15,"pt"))+
coord_cartesian(clip = "off")
Can’t find the diatom you want?
Contributions to DiatoViz package are welcome!
Please contact Gabriela Junqueira or submit a pull request.
We extend our gratitude to Sebastian Carl
for his creation of the nflplotR and nbaplotR packages, which played a
crucial role in shaping DiatoViz.
Kloster M., Kauer G. & Beszteri B. (2014): SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects. BMC Bioinformatics 15:218.