README.md

In svalvaro/drawCell: Generation of cell pictures

drawCell

The goal of drawCell is to easily obtain nice cell pictures in R!

Installation

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")

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:

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.

Examples

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"))

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