Here is a tool in development by the group of Ugur Dogrusoz at Bilkent University and colleagues to let you create the pathway diagrams.

http://pathwaymapper.org/

Many of the existing TCGA diagrams have been reproduced and you can overlay TCGA alteration data from cBioPortal using the site.

At the home screen choose "Collaborative" to create a pathway with a link that can be shared with others.

The tool allows you to both draw and export the diagrams in various forms. There is experimental option to allow you to export the pathways to SIFNX which can be read using the paxtoolsr Bioconductor package.

https://www.bioconductor.org/packages/release/bioc/vignettes/paxtoolsr/inst/doc/using_paxtoolsr.html

We'd be interested in hearing if you have other suggestions that would benefit R users, but we're unlikely to support the ability to generate the diagrams from R directly (automatically laying out these diagrams the way a person would is a hard problem).

Please file any bugs you find with the tool here: https://github.com/iVis-at-Bilkent/pathway-mapper/issues

From recent reactome release, you can download pathways as PPTX and edit in powerpoint.

http://reactome.org/PathwayBrowser/#/R-HSA-5205647