The goal of drawCell is to easily obtain nice cell pictures in R!
drawCell needs the package
webshot2, which needs to be
installed prior to the installation of drawCell.
To obtain the cell pictures, drawCell connects to the SwissBioPics
API so an internet connection is
required.
# install.packages("devtools")
devtools::install_github("svalvaro/drawCell")It requires the taxonomy id of your species of interest, and one or multiple SL codes for subcellular locations that will be colored. The SL codes for each subcellular location can be found at Uniprot and uniprotkb_sl2go.
To generate a cell of Homo sapiens (Taxonomy id: 9606) with
highlighted Endoplasmic Reticulum (SL code: 0095) and lipid droplets
(SL code: 0154):
library(drawCell)
drawCell(taxonomy_id = '9606', sl_ids = c('0095','0154'), color = 'yellow')
The taxonomy id for Quercus ilex a common tree in the south of Spain
is 58334 and as an example I will use the SL code of the chloroplast:
0049.
drawCell(taxonomy_id = '58334', sl_ids = '0049', color = 'lightgreen')
We can also obtain pictures of viruses, yeast, and pretty much everything that exists!
For the baker’s yeast Saccharomyces cerevisiae whose taxonomy id is
4932 we will highlight the nucleus: 0191 and the vacuole: 0272.
drawCell(taxonomy_id = '4932', sl_ids = c('0191', '0272'), color = 'pink')