No, unfortunately it contains functions etc. I'm not at liberty to publish. The section where I call the plot function in the .Rmd file is as follows:
x<-CustomScatterPlot()
where CustomScatterPlot() is just a wrapper of a ggplot with custom inputs. When I use this to produce a html directly the image appears fine, however, the problem arises when using the .Rmd to output a .md file. The above code produces the following chunk in the index.md file
### `CustomScatterPlot()`
<img src="index_files/figure-markdown_strict/unnamed-chunk-2-1.png" style="display: block; margin: auto;" />