Understanding the Issue with Plotly in R Markdown using source()

In this article, we’ll explore the issue of why Plotly plots work fine when run directly from an R script but fail to render correctly when used within a source() block in an R Markdown document. We’ll also delve into the specifics of how Plotly works and what might be causing these issues.

What is Plotly?

Plotly is a popular data visualization library that allows users to create interactive plots, charts, and other visualizations for their data. It supports a wide range of chart types, including line plots, scatter plots, bar charts, and more.

The Problem with source() in R Markdown

The problem lies in how Plotly handles its output when embedded within an R Markdown document using the source() function. When you run an R script directly from the command line or an IDE, Plotly’s output is rendered as HTML code that can be displayed in a web browser.

However, when you use source() to load an R script within an R Markdown document, Plotly’s output is not rendered correctly. This results in an error message indicating that at least one layer must contain all faceting variables.

Understanding Faceting Variables

In the context of Plotly and ggplot2 (another popular data visualization library in R), faceting refers to the process of dividing a dataset into separate groups based on specific variables. When you facet your data, each group is represented as a separate plot layer.

Faceting is an important feature of many data visualizations, allowing users to compare different subsets of their data. However, when using Plotly and facet_wrap(), it’s essential that all faceting variables are included within the same plot layer to avoid rendering errors.

The Role of chunk_output_type in R Markdown

The chunk_output_type parameter is used in R Markdown documents to control how output from chunks (blocks of R code) is rendered. In this case, we’re using chunk_output_type: console, which tells R Markdown to display the output as a console or command line.

However, Plotly’s behavior when rendering within an R Markdown document doesn’t quite align with this setting. When chunk_output_type is set to console, it can lead to issues like the one we’re experiencing here.

Troubleshooting and Solution

To resolve the issue of Plotly not working correctly in your R Markdown document, you’ll need to try a few things:

Check if all faceting variables are included within the same plot layer.
Ensure that chunk_output_type is set correctly.
Try setting chunk_output_type to html or another value that allows Plotly’s HTML output to be rendered.

Here’s an updated version of your R Markdown document with these changes applied:

---
title: "RPE_Dashboard"
output:
  flexdashboard::flex_dashboard:
    vertical_layout: fill
editor_options:
  chunk_output_type: html
---

By making this change, we’re instructing R Markdown to render the output as HTML code, which Plotly can use to display its plots correctly.

Conclusion

Plotly is a powerful tool for creating interactive data visualizations in R. However, when used within an R Markdown document via source(), it may not render correctly due to issues with faceting and chunk output types.

By understanding how Plotly works and what might be causing these issues, you can troubleshoot and resolve problems like this one. Remember to check that all faceting variables are included within the same plot layer and ensure that your chunk_output_type is set correctly for optimal results.

Example Use Case

Here’s an example of a working R Markdown document with Plotly:

---
title: "RPE_Dashboard"
output:
  flexdashboard::flex_dashboard:
    vertical_layout: fill
editor_options:
  chunk_output_type: html
---

library(flexdashboard)
library(tidyverse)
library(plotly)

# Load the data

rpe_summary <- read.csv("data/rpe_data.csv")

# Create a Plotly plot

plot_1 <- rpe_summary %>%
  ggplot(aes(Date, RPE)) + 
  geom_col() + 
  labs(title = "RPE for the Week",
       x = "",
       y = "") +
  facet_wrap(~Name, scales = "free")

# Convert to Plotly

plot_1 <- plot_ly(plot_1, type = 'scatter', mode = 'lines',
                 hovertext = ~paste("Date:", Date, "\nRPE:", RPE),
                 text = ~ paste("Date:", Date, "\nRPE:", RPE)) %>%
  layout(title = "RPE for the Week")

# Display Plotly

plot_1

In this example, we load a dataset and create a simple Plotly plot using ggplot2 and plotly. The resulting plot is interactive and should be displayed correctly in your R Markdown document.

Last modified on 2024-09-24