In svalvaro/drawCell: Generation of cell pictures

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Overview

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.

Installation

Install dev version of drawCell:

# install.packages("devtools")
devtools::install_github("svalvaro/drawCell")

How to use

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.

Examples

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"))

svalvaro/drawCell documentation built on Nov. 22, 2022, 5:29 p.m.