Producing a Word document using RMarkdown with programmatically-generated, interleaved, headers and graphs

Background: Using Purrr to filter a dataset and plot a series of graphs using ggplot (in RMarkdown, for Shiny)

Following the resolution of the previous question, above, I now have a .Rmd file that will produce a Word document with section headers, graphs, and a table of contents.

The following problems remain:

1. The section headers and graphs are not interleaved. What I currently have is:

header1

header2

header3

graph1

graph2

graph3

How should my code be amended to produce:

header1

graph1

header2

graph2

header3

graph3

instead?

2. The word document includes numbers in square brackets, e.g. "[[1]]", "[[2]]", etc, which I believe get printed with the graphs. How can these be removed?

3. For each graph I'd like a boilerplate sentence that includes a statement about the data, specifically the number of datapoints that lie outside the dotted lines +/- 2SD from the mean. I've tried adding it by including e.g.

report.data %>% 
dplyr::filter(identifier == x) %>%
paste(eval("r sum(result < mean(result) - 2 * sd(result))"), " results out of bounds.") 

in the function, but this turns the graphs into text(!).

As always, any help or advice that can be offered would be greatly appreciated - thank you for reading!

Script to generate example data and produce the report:

library(dplyr)
set.seed(1234)

test1.level1.analyser1 <- data.frame(
  result = rnorm(25, mean = 2.5, sd = 0.2), 
  test = c("test1"), 
  level = c("level1"), 
  sample.no = c(1:25), 
  analyser = c("analyser1")
  )

test1.level1.analyser2 <- data.frame(
  result = rnorm(25, mean = 2.6, sd = 0.1), 
  test = c("test1"), 
  level = c("level1"), 
  sample.no = c(1:25), 
  analyser = c("analyser2")
  )

test1 <- rbind(test1.level1.analyser1, test1.level1.analyser2)

test2.level1.analyser1 <- data.frame(
  result = rnorm(25, mean = 10, sd = 2), 
  test = c("test2"), 
  level = c("level1"), 
  sample.no = c(1:25), 
  analyser = c("analyser1")
  )

test2.level1.analyser2 <- data.frame(
  result = rnorm(25, mean = 9.5, sd = 0.75), 
  test = c("test2"), 
  level = c("level1"), 
  sample.no = c(1:25), 
  analyser = c("analyser2"))

test2.level2.analyser1 <- data.frame(
  result = rnorm(25, mean = 30, sd = 1.8), 
  test = c("test2"), 
  level = c("level2"), 
  sample.no = c(1:25), 
  analyser = c("analyser1")
  )

test2.level2.analyser2 <- data.frame(
  result = rnorm(25, mean = 25, sd = 0.75), 
  test = c("test2"), 
  level = c("level2"), 
  sample.no = c(1:25), 
  analyser = c("analyser2"))
test2.level2 <- rbind(test2.level2.analyser1, test2.level2.analyser2)

test2 <- rbind(test2.level1, test2.level2)

write.csv(test1, "test1.csv", row.names = FALSE)
write.csv(test2, "test2.csv", row.names = FALSE)

###
report.data <- rbind(test1, test2) %>% mutate(identifier = paste(test, level, sep = " ")) 
rmarkdown::render("report.Rmd", params = list(report.data = report.data), output_file = "intersite.comparison.report.doc")

The report.Rmd file:

---
title: "Inter-site IQC Comparison Report"
output: word_document
toc: yes
---

```{r setup, include=FALSE, comment = "", results = 'asis', echo = FALSE}
library(dplyr)
library(ggplot2)
library(purrr)
knitr::opts_chunk$set(echo = FALSE)

 my_plot <- function(df) {
    ggplot(df, aes(x = sample.no, y = result)) +
    geom_point(aes(colour = analyser)) +
    geom_hline(aes(yintercept = mean(result) + 2 * sd(result)), colour = "red", linetype = "dashed") +
    geom_hline(aes(yintercept = mean(result) - 2 * sd(result)), colour = "red", linetype = "dashed") +
    theme_classic() +
    theme(legend.title = element_blank()) +
    labs(
      # the title above the plot, based on information in the filtered df
      title = paste0("Inter-site comparison for ", unique(df$identifier)),
      x = "Sample number",
      y = "Result",
      # the text below, based on data in the filtered data frame
      caption = paste0("Caption here.")) +
    expand_limits(y = 0) +
    coord_cartesian(xlim = c(0, max(df$sample.no) + 2)) +    
    theme(
      # configure the caption / sentence below
      plot.caption=element_text(size=12, hjust = 0, margin = margin(t=20)),
      # add some buffer at bottom as spacing between plots
      plot.margin = margin(b=50)
    )
}
```

```{r, comment = "", results = 'asis', echo = FALSE}
purrr::map(unique(report.data$identifier),
                           function(x) {
                             #section heading
                             cat("#", (x), "\n")
                             # filter data before passing it to the plot function
                             report.data %>% 
                               dplyr::filter(identifier == x) %>%
                               my_plot()
                             #report.data %>% 
                               #dplyr::filter(identifier == x) %>%
                               #paste(eval("r sum(result < mean(result) - 2 * sd(result))"), " results out of bounds.")
                           }
)
```

EDIT: the current version of the code for the map function, following Sean van der Merwe's kind advice, below:

purrr::map(unique(report.data$identifier),
                           function(x) {
                             #section heading
                             cat("#", (x), "\n")
                             cat("\n\n")
                             # filter data before passing it to the plot function
                             report.data %>% 
                               dplyr::filter(identifier == x) %>%
                               my_plot() %>% print()
                             cat("\n\n")
                             #report.data %>% 
                               #dplyr::filter(identifier == x) %>%
                               #paste(eval("r sum(result < mean(result) - 2 * sd(result))"), " results out of bounds.")
                           }
) -> results