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talgalili / heatmaply

Interactive Heat Maps for R Using plotly
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Exporting heatmaply plot to .pdf - orca installation not found #242

Closed kleurless closed 4 years ago

kleurless commented 4 years ago

Hi,

I've opened this issue yesterday on orca's github, but I was wondering if some of you might have run into the same problem?

I installed orca in a conda environment (SSH server, so I can't install as a stand-alone binary) and the installation succeeded, but when I try to export my plot it still gives me the error that I have to install orca. I have also tried to install orca as a stand-alone binary on my Windows laptop, but it won't recognize orca as a program or command (and yes, I have followed each step of adding orca to my PATH thoroughly; even executed it ~5 times); ergo, same problem.

Is anyone experiencing the same problem? Or does anyone know a different way to export the plot to a .pdf? The jpeg/png/bmt resolution is just way too low. Thanks in advance!

alanocallaghan commented 4 years ago

I've not had issues with orca but I haven't had to work with it in conda.

Have you tried passing vwidth and vheight, or zoom to plotly::export? That should increase resolution

kleurless commented 4 years ago

@Alanocallaghan plotly::export exports empty images for me, so I'm not sure that that would work.. Do you remember how you installed orca?

alanocallaghan commented 4 years ago

Not really, I don't tend to use conda so I probably installed the AppImage somewhere on my path. I don't have it installed at the moment

Can you provide some example code and output from what you've tried so far?

alanocallaghan commented 4 years ago

(I did have the orca screenreader installed however which is always a fun thing to discover :) )

kleurless commented 4 years ago

This is the code that I use to make my plot:

p <- heatmaply_cor(cor(as.matrix(mtcars)))

And I have tried the following codes to export: 1: orca(p, file="my_plot.pdf") 2: plotly::export(p, file="my_plot.pdf") 3: adding file="my_plot.pdf" to the heatmaply_corr command above

They give the following results: 1:

Error: The orca command-line utility is required for this functionality.

Please follow the installation instructions here -- https://github.com/plotly/orca#installation
Execution halted

2: An empty .pdf (also with .jpeg, or any other extension).

3: Again an empty .pdf, together with the following output on screen:

Warning messages:
1: In value[[3L]](cond) : plotly::orca failed:
 Error: The orca command-line utility is required for this functionality.

Please follow the installation instructions here -- https://github.com/plotly/orca#installation

2: 'plotly::export' is deprecated.
Use 'orca' instead.
See help("Deprecated")

Besides that, I have tried to install orca as a stand-alone binary on my computer, following these steps. But at the final step, where you check if the executable is available, it fails:

'orca' is not recognized as an internal or external command, operable program or batch file.

And I succesfully installed orca in conda using conda install -c plotly ploty-orca, but then it still gives the error at nr1.

alanocallaghan commented 4 years ago

No idea. If I install orca in a conda environment it works fine. It also works fine if I chmod +x the app and move it into /usr/local/bin. I appreciate this is frustrating but I don't know enough about orca to act as tech support here.

Only suggestion I have is to check if the install directory is in your path before and after starting R