CODEWITHSUNDEEP
rggplot2latexknitrkable
carolinasc
carolinasc

Reputation: 79

Knitr not printining the plots in a loop

I'm using Knitr to generate a PDF report, where each page is dynamically created in a loop, displaying plots and tables side by side. The approach works well for tables, but the plots fail to appear in the output.

I'm using ggsurvminer and storing plots in a list, then attempting to print them inside the loop. However, while tables render correctly, the plots do not show up in the final document.

Here’s a MRE illustrating the issue:

#```{r config, include=FALSE}
newslide <- function(content) {
  code <- deparse(substitute(content))

  cat(sep = "\n",
    knitr::knit_child(
      quiet = TRUE,
      text = c("```{r dpi=600, warning=FALSE, message=FALSE, echo=FALSE, results='asis', escape = TRUE}",
    code, 
    "```")
      )
  )
}
#```

#```{r latex, echo=FALSE, results = 'asis', escape = "TRUE"}
plot_list <- list()
category <- c("A","B","C")

for (cat in category){
  fit <- survfit(Surv(time, status) ~ sex, data = lung)
  p <- ggsurvplot(fit, data = lung)
plot_list[[cat]] <- p
}

for (cat in category){
  plot1 <- plot_list[[cat]]$plot #I've also tried without "$plot"
  table1_latex <- kable(head(lung), format = "latex")
      newslide(
  content = {
        cat("\\begin{multicols}{2}\n")
        cat("\\noindent\n")
        print(table1_latex)
        cat("\\columnbreak\n")
        cat("\\begin{center}\n")
        print(plot1)
        cat("\n")
        cat("\\end{center}\n")
        cat("\\end{multicols}\n")
  }
)
}

I'm getting this error message when knitting:

! Missing $ inserted.
<inserted text> 
                $
l.561 ![](rewrite_
                  files/figure-latex/unnamed-chunk-19-1.pdf)<!-- -->

Thank you in advance for any suggestions.

Upvotes: 3

Views: 60

Answers (1)

carolinasc
carolinasc

Reputation: 79

I solved it by adding cat('\n\n') directly after printing the plot.

Upvotes: 3

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