# Share interactive heatmaps to collaborators

#### Zuguang Gu ( z.gu@dkfz.de )

#### 2022-04-26

For JavaScript-based interactive heatmaps, all necessary files (html, js and css files) can be saved to disk and interactive heatmaps can be opened in another computer without R being installed. But InteractiveComplexHeatmap is different. The interactivity of InteractiveComplexHeatmap is implemented with shiny, ComplexHeatmap and other related R packages, which means, R must be installed on computers where interactive heatmaps are going to be opened. Nevertheless, there are the following two ways that can used to share interactive heatmaps generated by InteractiveComplexHeatmap.

## The `save` argument

In `htShiny()`, there is a `save` argument which can be set to a path of a folder where interactive heatmap files are stored.

    # E.g. the folder is "test_ht"
    htShiny(ht, save = "test_ht")

Then in the folder `test_ht`, there are the following files generated:

    guz@B069-mb04:~/test_ht$ ls -l
    total 40
    -rw-r--r--  1 guz  staff   1.1K Oct 18 15:19 htShiny.R
    -rw-r--r--  1 guz  staff   5.9K Oct 18 15:19 htShiny.RData
    -rw-r--r--  1 guz  staff    18B Oct 18 15:19 htShiny.bat
    -rw-r--r--@ 1 guz  staff    18B Oct 18 15:19 htShiny.sh

`htShiny.R` contains R code that generates the interactive heatmap. `htShiny.RData` contains all R objects needed for heatmap and it will be loaded in `htShiny.R`. The other two files `htShiny.sh` and `htShiny.bat` are basically identical and they can be run in the terminal under Linux/MacOS or Windows.

The four files can be sent to collaborators and they can run the following commands to open the interactive heatmap:

    cd ~/test_ht
    sh htShiny.sh
    # or
    Rscript htShiny.R

Under Windows, they can simply double click `htShiny.bat`.

Executing `htShiny.sh` or `htShiny.bat` prints a message where collaborators can find the link and paste it to browser to open the interactive heatmap.

    guz@B069-mb04:~/test_ht$ sh htShiny.sh
    If the shiny app is not automatically opened in the browser, you can manually
    copy the following link and paste it to the browser.
    Listening on http://127.0.0.1:4132

Note, on the collaborator’s side, R must be installed (however, they don’t need to directly interact with R). If the InteractiveComplexHeatmap package is not yet installed there, `htShiny.R` automatically installs it for them.

## Use Shiny Server

It would be much easier if there is already a Shiny Server available. Users simply put all code that generates interactive heatmaps into a script named `app.R`. Under RStudio, they execute the script and click “Publish” in the Shiny app window.

Or under command-line:

    rsconnect::setAccountInfo(...)
    rsconnect::deployApp(...)

Check https://shiny.rstudio.com/deploy/ to find out how to publish Shiny apps to Shiny Server.

Please note, in the R session which publishes the Shiny app, you must execute the command `setRepositories(ind = 1:4)` so that on the Shiny Server side, it can successfully install InteractiveComplexHeatmap package.

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