Instead of having to include the relative path to an image like so:

![\label{fig:R1amb}R1 Ambient RNA Contamination](../outs/pre-processing/ambientRNA_R1.png)

I would like to bring in an image from the yaml object like so:

![\label{fig:R1amb}R1 Ambient RNA Contamination](`r yaml$inputs$R1_ambient`)

where yaml$inputs$R1_ambient contains the full path to the png. However, this does not render the image. Why is that?

CodePudding user response：

I'm not sure which flavour of Rmarkdown you're using (so not sure about yaml$inputs and the label cross-reference). However, my solution should work nevertheless.

You can use knitr::include_graphics in an R chunk to make use of the parameterised path:

---
title: "Test"
date: "4/4/2022"
output: html_document
params:
  R1_ambient: "test.png"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Plot
```{r R1amb, echo = FALSE, fig.cap = "R1 Ambient RNA Contamination"}
knitr::include_graphics(params$R1_ambient)
```