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gofigR

gofigR is the R client for https://gofigr.io, a zero-effort reproducibility engine. It works with any R library which outputs to R graphics devices, with automatic publishing for ggplot.

Compatibility

gofigR integrates with R markdown, both in knitr and in interactive sessions in RStudio. GoFigr also works in scripts. We tested with R 4.3.2 but any reasonably recent version should work.

GoFigr will automatically publish all ggplot output assuming you call gofigR::enable(auto_publish=TRUE). GoFigr will not publish old-style R plots unless you tell it to. See the “Usage” section below.

Installation

library(devtools)
devtools::install_github("gofigr/gofigR")

Configuration

On the R prompt, simply load the gofigR package and call gfconfig(). You only need to do this once.

If you don’t have an account, you can register at https://app.gofigr.io/register.

> library(gofigR)
Attaching package: ‘gofigR’

> gfconfig()
-------------------------------------------------------------------

Welcome to GoFigr! This wizard will help you get up and running.

-------------------------------------------------------------------


Username: publicdemo
Testing connection...

  => Success

API key (leave blank to generate a new one): 
Key name (e.g. Alyssa's laptop): my API key
Fetching workspaces...

1. Scratchpad - e5249bed-40f0-4336-9bd3-fef30d3ed10d

Please select a default workspace (1-1): 1

Configuration saved to /Users/maciej/.gofigr. Happy analysis!

Usage

To enable GoFigr, simply call enable in your setup chunk. You can also optionally specify an analysis_name (it will be created automatically if it doesn’t exist).

```{r setup, include=FALSE}
library(gofigR)
gofigR::enable(auto_publish=TRUE)
```

auto_publish is FALSE by default. Set it to TRUE to override plot and print and publish figures automatically.

Automatic output capture

If auto_publish is on, GoFigr will intercept all calls to plot and print and publish the results if they are from a compatible library. At the moment, we support any graphics format also supported by ggplotify:

Manual capture

To capture output manually, simply call publish:

hm1 <- Heatmap(matrix(rnorm(100), nrow=10, ncol=10))

publish(hm1, "Heatmaps are cool!")  # second argument is the figure name

Capturing base graphics

To capture output from base R plotting, call publish_base:

gofigR::publish_base({
  base::plot(pressure, main="Pressure vs temperature")
  text(200, 50, "Note the non-linear relationship")
}, data=pressure, figure_name="Pressure vs temperature")

gofigR::publish_base({
  # The mtcars dataset:
  data <- as.matrix(mtcars)

  coul <- colorRampPalette(brewer.pal(8, "PiYG"))(25)
  heatmap(data, scale="column", col = coul, main="Visualizing mtcars")
}, data=mtcars, figure_name="Cars")

Note the optional data argument following the expression. It specifies the data which you want to associate with the figure – it will show up under “files” (as .RDS) once published.

Interactive use

We support knitr as well as interactive sessions in RStudio.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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