problem with Rmd script and showing plots in chunk output and in final report html

Hello everyone!

I am developing an R Markdown (Rmd) script in which I need to create ggplot2 plots using the facet_wrap and geom_jitter parameters. After creating each plot in a different chunk, the resulting plot is being displayed in the Viewer panel of RStudio. It is not showing in the chunk output, even though I have added the parameters "'hold'" and "echo=TRUE" to the chunk configuration. (I have also added them to the YAML configuration in the Rmd).

As another peculiar detail, when I try to run ggplotly on this plot, the final configuration changes and distorts the entire graph, making it hard to interpret.

I have also attempted to remove the plots from memory using and, but that did not change anything.

As a last option, I reviewed the general chunk options in the Rmd, and "Chunk Output Inline" was selected, along with "Preview Images and Equations" and "Show Previews Inline".

I would appreciate any help.



Welcome to the forum

I think we need to see your code and some sample data. See
FAQ Asking Questions

A handy way to supply some sample data is the dput() function. In the case of a large dataset something like dput(head(mydata, 100)) should supply the data we need. Just do dput(mydata) where mydata is your data. Copy the output and paste it here between


What operating system are you using?


First of all, I apologize for the late response and the next problem: I cannot provide any sample data.

About my operating system: I am working on Ubuntu Linux 22.04, and the graphs that were giving me problems had the following structure:

p9 <- ggplot(datos_long, aes(x = varInte, y = Measure, fill=varint)) +
  geom_boxplot(outlier.shape  = NA) +
  geom_jitter(aes(color = varint), height = 0, width = .2) +
  labs(x = "varInte", y = "Measure\n") +
  facet_wrap(~ varint, scales = "free") +
  theme_minimal() +
  theme(legend.position = "right",
        axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1, size = 7),
        plot.background = element_rect(size = 2, color = "white"),
        plot.margin = unit(c(1, 1, 1, 1), "cm"),
        strip.text.x = element_text(size = 6),  
        legend.title = element_text(size = 8),
        legend.text = element_text(size = 6))  +
        labs(fill = "vartInte") + 
  guides(color = FALSE, fill = guide_legend(override.aes = list(size = 1)))  


I have renamed the variable's names. Also, if this could work in any way, I transformed the dataset into a long one to represent the data. The data I wanted to represent is related to the abundance (Measure) of bacteria genera (varint) against a variable of interest from the metadata (varInte).

I finally made it work using the command ggsave() followed by the command knitr::include_graphics().

However, I still cannot understand why if I don't use these combined commands, it doesn't work.

Thank you so much for your response!


Sorry for the late reply. I came down with something like the flu.

I have no idea of why you need those commands. Where do you place them? In any case I am getting the same blank output without them.

If I run the code with some mocked up data under normal R I get what looks to be very weird results. See below.


It just occured to me.
In ```{r } is include set to TRUE ?

That is, you may want something like this

insert code


I have only echo=FALSE and some parameters related to the fig size (width, height,...). I have also tried with the parameters: with and fig.align = "center".

I will check the options you gave me and update you with news.


Blast it, I was in a hurry and did not realize I messed up my code

```{r include = TRUE}
insert code

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