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datapplab / pathview

pathway based data integration and visualization
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Printing the Pathview Output on RMarkdown Document #20

Closed canholyavkin closed 1 year ago

canholyavkin commented 2 years ago

I'm using pathview on the Rmarkdown document. However, pathview() just saves a plot into the current directory. Is it possible to display the output of pathview() directly in R?

joseale2310 commented 2 years ago

I would also like to know how to save all the results to another directory. Setting kegg.dir = "../Results/" only saves the png and xml, but the "Id.pathway.png" image is still saved in the current directory!

joseale2310 commented 2 years ago

@canholyavkin You could use knitr::include_graphics("path/to/pathway.png") to see the result in the Rmarkdown

canholyavkin commented 2 years ago

@canholyavkin You could use knitr::include_graphics("path/to/pathway.png") to see the result in the Rmarkdown

Unfortunately, I also execute the pathway analysis on the same RMarkdown, so the png images are not generated at the beginning of the render. So, as the R couldn't find the png images in the first check, it just gives an error.

raw937 commented 1 year ago

Are you still having this issue?

This project is no longer under development here. Please check the new fork here. https://github.com/Kannapolis-Bioinformatics/pathview

If you have the same issues place in: https://github.com/Kannapolis-Bioinformatics/pathview/issues

many thanks, Rick

canholyavkin commented 1 year ago

I'll check the issue again and if it persists I'll open a case at new repo. Thanks.

joseale2310 commented 1 year ago

Somehow I cannot place issues there, only pull requests! Are issues disabled in the repo? https://github.com/Kannapolis-Bioinformatics/pathview/

raw937 commented 1 year ago

Fixed now.