The goal of drawCell is to easily obtain nice cell pictures in R!
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")You can use drawCell in two ways, one is to use the Web application created with Shiny. We will have this app deployed soon. You can run it locally with:
drawCell::drawCellShiny()If you want to get the cells pictures in your Rmarkdown documents,
reports, you just need to use the main function 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(organism_identifier = '9606', list_sl_colors = list("SL0173" = "red", "SL0101" = "blue"))The organism_identifier 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(organism_identifier = '58334', list_sl_colors = list("SL0049" = 'lightgreen'))We can also obtain pictures of viruses, yeast, and pretty much everything that exists!
For the baker’s yeast Saccharomyces cerevisiae whose
organism_identifier is 4932 we will highlight the nucleus: 0191
and the vacuole: 0272.
drawCell(organism_identifier = '4932', list_sl_colors = list("SL0191" = "pink", "SL0272" = "yellow"))