call RMarkdown on command line using a.R that is passed a file
It's not entirely clear what you are trying to do. It seems like you have a text file which has to be converted to an Rmd by an R script (why isn't it just an Rmd to begin with?) and then you want to render the Rmd. You can do this by running these commands in your terminal:
Rscript Graphs.RRscript -e "rmarkdown::render('output_file.Rmd')"The first command runs the Graphs.R file which presumably generates output_file.Rmd. The second command runs a one-liner which knits output_file.Rmd into output_file.html.
If you want to read command line arguments in an R file, try ?commandArgs.
args <- commandArgs(trailingOnly = TRUE)Also see this Stack Overflow question.