knitr::opts_chunk$set( collapse = TRUE, comment = "#>", message = FALSE, warning = FALSE, purl = FALSE )
The package drawCell provides the functionality to generate cell pictures with highlighted subcellular organelles with R.
It uses the SwissBioPics API so an internet connection is required to use this package.
Install dev version of drawCell
:
# install.packages("devtools") devtools::install_github("svalvaro/drawCell")
It is fairly simple to use drawCell
. You just need to know the
organism_identifier
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.
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
.
The size of the picture can be chosen with size
and the colour_sl with colour_sl
.
library(drawCell) drawCell(organism_identifier = '58334', list_sl_colors = list("0049" = "red"))
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" = "brown", "SL0272" = "pink"))
If one wishes to highlight the endosomes (SL:0101) of Homo sapiens (organism_identifier: 9606):
drawCell(organism_identifier = "9606", list_sl_colors = list("SL0101" = "blue"))
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