mattjmeier
commented
4 weeks ago Apologies for the confusion. If you want to retain separate color and shape encodings (one by chemical and one by dose), then creating a single combined legend label isn't the best approach because it would not maintain the separate visual encodings.
Plotly's default legend behavior will create separate entries for each unique combination of color and symbol. It seems Plotly is currently creating multiline text entries for legend items that combine color and symbol due to some internal formatting issues.
To fix this and ensure your legend labels remain on a single line, you may have to create a custom legend. Unfortunately, managing the legend entries manually can be quite involved and is not directly supported through the plotly API for R.
Therefore, another approach would be to shift the symbol (shape) legend outside the plot area and deal with these two legend items (color, symbol) separately. This would prevent Plotly from combining color and symbol into the same legend entry.
Here's an example of how you might update your code to implement this:
# Your original code to set up the plot
p_pca <- plot_ly(data = pca_data, type = "scatter", mode = "markers",
x = ~PC1, y = ~PC2,
color = as.formula(paste0("~", expgroup1)),
symbol = ~level, text = ~sample,
size = 3) %>%
layout(title = "PCA of Experimental Samples",
xaxis = list(title = paste0("PC1 (", round(100 * summary(pca_result)$importance[2, 1], 1), "%)")),
yaxis = list(title = paste0("PC2 (", round(100 * summary(pca_result)$importance[2, 2], 1), "%)")),
legend = list(x = 1.1, y = 1, xanchor = "left", yanchor = "top", orientation = "v"))
# Highlight functionality remains unchanged
plotly::highlight(p_pca, on = "plotly_click", off = "plotly_doubleclick", color = "red")
# Custom legends are not straightforward in plotly, so we'll work around by breaking
# up the color and symbol legends and positioning them manually, if necessary.
To manually control the placement of the legend, you can use x and y attributes of layout(legend = list( ... )). The above code attempts to place the legend to the right of the plot (assuming there's space), but you can adjust x and y to position it elsewhere.
If your issue persists or Plotly isn't respecting these settings due to some internal formatting logic, an alternative might be to modify the column names before they're output to the legend, removing any characters that might be causing line breaks. However, plotly generally tries to respect space constraints and may still use multiline labels if the legend items don't fit in the provided space. In that case, consider making the plot area smaller or increasing the area available for the legend.
Lastly, ensure that you're using the latest version of Plotly for R, as there may have been bug fixes and improvements that affect legend formatting. If the issue persists and none of these solutions suffice, you might have to file an issue with the Plotly R library's maintainers to seek a resolution.
In a Plotly chart, when you're using both color and symbol as encoding for your data points, Plotly may automatically create a legend that tries to show all possible combinations, which can become problematic if you have many unique combinations.
Customizing the legend text in a Plotly scatter plot isn't directly supported through plot_ly's basic arguments, but you can change the structure of your data before creating the plot to get around this limitation. Here's how you might do it:
First, create a new column in your pca_data data frame that combines the information from the color and symbol factors into a single string. Use this new column as the basis for your legend by assigning it to the name argument within plot_ly. Here's how you can modify your code snippet to implement these changes:
Remember to adjust the paste function call to fit your actual variables and desired separator. If expgroup1 or exp_group2 are more than one column, then you might need to adapt the code to concatenate the values from those columns into a single string for each row in pca_data.