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When working with the vitessceR package, you may encounter issues, particularly related to file formatting, file permissions, URL typos, etc. Below, we list some debugging methods that may help to resolve these bugs.

If none of these tips help, please write an issue on GitHub.

The following code snippets assume that vitessceR has been loaded via library(vitessceR) and the Vitessce configuration instance is stored in the variable vc:

library(vitessceR)
vc <- VitessceConfig$new("My single-cell data visualization")

Use the out_dir parameter for data object wrapper classes

Rather than using a temporary directory, this will write converted files to the specified directory. This way, you can open and explore the converted output files.

dir.create("./debug")

dataset <- vc$add_dataset("My dataset")
dataset <- dataset$add_object(SeuratWrapper$new(pbmc3k.final, out_dir = "./debug"))

Use the port parameter

vc$widget(port = 9000)

Add the status component to the layout

status <- vc$add_view(dataset, Component$STATUS)
vc$layout(hconcat(scatterplot, status))

Write the configuration to JSON

vc_list <- vc$to_list()
jsonlite::toJSON(vc_list, auto_unbox = TRUE)

Open the browser console

If the Vitessce widget loads in the RStudio "Viewer" tab, but the data fails to load or there are issues related to the user interface, you can open the browser console to check for errors or warning messages.

To do so, right click in the Viewer area and select "Inspect Element."

Then, click "Console" in the inspector window that appears.