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.
``` {r installation, eval= FALSE}
devtools::install_github("svalvaro/drawCell")
## Usage 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: ``` {r shinyApp, eval= FALSE} 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"))
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