Pluto R package

A simple R interface for interacting with data and results stored in Pluto, the collaborative life sciences platform.

Create your API token

If you are accessing data programmatically for the first time, you'll need to generate a new API token. Navigate to your Account page in Pluto and click the "+ API token" button.

A new API token will be generated, and can then be copied or viewed.

This API token can be used to fetch data programmatically using this R package.

Set up R environment

1. Set the PLUTO_API_TOKEN environment variable

Copy the API token that you created on your Account page and store it in an environment variable called PLUTO_API_TOKEN. To do this, create an .Renviron file containing:

PLUTO_API_TOKEN="<YOUR API TOKEN>"

2. Source the latest version of the R package

# Load required dependencies
library(httr)
library(jsonlite)
library(rjson)

# Print PLUTO_API_TOKEN to confirm that it's in your environment
Sys.getenv('PLUTO_API_TOKEN')

# If PLUTO_API_TOKEN is blank, make sure the API key is in .Renviron
# and restart your R session, then rerun Sys.getenv('PLUTO_API_TOKEN')

# Import the pluto_read() function
devtools::source_url("https://github.com/pluto-biosciences/pluto-sdk-R/blob/main/pluto.R?raw=TRUE")

Fetch data from Pluto

Sample data

sample_data <- pluto_read(experiment_id = 'PLX140206', 
                          data_type = 'sample')

# All 12 rows of the sample data were fetched

Assay data

assay_data <- pluto_read(experiment_id = 'PLX140206', 
                         data_type = 'assay')

# Paginating API calls to retrieve all 32544 rows in the assay data in batches of 10000 rows... 
# Fetching rows 10001 to 20001... 
# Fetching rows 20001 to 30001... 
# Fetching rows 30001 to 32544...

Plot data (results)

Visit our website to learn more about the assays and analyses that Pluto supports. To fetch data from a specific analysis and plot, obtain the plot ID from the Methods Modal on any plot:

Use the plot ID in the pluto_read() function to fetch the underlying results:

deg_table <- pluto_read(experiment_id = "PLX140206", 
                        plot_id = "386b3bbf-fc86-4071-88c2-6340634cdc62",
                        data_type = "results")

# Paginating API calls to retrieve all 16954 rows in the assay data in batches of 10000 rows... 
# Fetching rows 10001 to 20001...

Available endpoints

For more information about all available endpoints, visit the Pluto API docs