You may be interested in the knitr function spin_child(). It can be used to insert R scripts as if they were code chunks in an R Markdown file.
To demonstrate, I created an R script called analysis.R that contained:
plot(rnorm(100))
And a template R Markdown file that contained:
---
title: "Insert R as Code Chunk"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
`r knitr::spin_child("analysis.R")`
When I knit the file to HTML, the code in the R script appears as if it was a chunk in the R Markdown file:
