Create multiple plots with unique RMarkdown headers

Question

Using spineplot in R, I am trying to create a series of plots that compare some potential covariates against age categories so we can do some preliminary data exploration. I have this code written up in R Markdown and I am using RStudio to knit the file into an HTML output. However, I am having difficulty getting each plot produced by my loop to have an appropriate RMarkdown header. I have tried putting cat("## my header") in the loop that produces each plot, but for some reason it only shows up for the first plot, and not the rest. It prints out for the rest of them, but does not get interpreted as Markdown.

Here's an example of my code:

---
title: "Minimal Working Example"
author: "TARehman"
date: "Wednesday, August 27, 2014"
output:
  html_document:
    toc: yes
---

# Spineplots
```{r mwe, echo=FALSE, results='asis', fig.height=5, fig.width=8, dpi=300}
tempdata <- data.frame(age=c("0-1","0-1","1-3","1-3","3-7","10-15","3-7","7-10"),
                       covA=c("Class 0","Class 1","Class 3","Class 2","Class 4","Class 3","Class 1","Class 2"),
                       covB=c("Class 1","Class 3","Class 2","Class 4","Class 4","Class 1","Class 1","Class 0"),
                       covC=c("Class 3","Class 3","Class 2","Class 3","Class 1","Class 4","Class 4","Class 4"))

temp_covars <- c("covA","covB","covC")

temp_locvec <- c(0.1,0.3,0.5,0.7,0.9)
temp_labvec <- c("0-1","1-3","3-7","7-10","10-15")
temp_colvec <- rainbow(n = 5,start = 7/12,end = 9/12,alpha = 0.8)

for(x in temp_covars) {

    cat(paste("## Spineplot of",x,"vs. age groups\n",sep=" "))

    spineplot(x = tempdata[[x]],
              y = tempdata$age,
              ylab = "Age Group",
              xlab = "Class",
              col = temp_colvec,
              off = 0,
              yaxlabels = c(NA,NA,NA,NA,NA),
              main = paste("Classes of",x,"versus age groups",sep=" "))

    for(j in 1:5) {
        axis(side = 2,
             at = temp_locvec[j],
             labels = temp_labvec[j],
             col.axis = temp_colvec[j],
             font.axis = 2)
        }
    rm(j)
}
rm(list=c("x","temp_locvec","temp_labvec","temp_colvec"))
```

The output looks like this.

Answer 1

It turns out that you need an extra carriage return. As Yihui pointed out, a header needs a blank line before it to be interpreted correctly by Markdown. Adding a simple cat("\n\n") to the end of my loop fixes things.

I had tried only adding one line break, but missed that two were needed to get the header to be interpreted correctly.

---
title: "Working Solution"
author: "TARehman"
date: "September 3, 2014"
output:
  html_document:
    toc: yes
---

# Spineplots
```{r mwe, echo=FALSE, results='asis', fig.height=5, fig.width=8, dpi=300}
tempdata <- data.frame(age=c("0-1","0-1","1-3","1-3","3-7","10-15","3-7","7-10"),
                       covA=c("Class 0","Class 1","Class 3","Class 2","Class 4","Class 3","Class 1","Class 2"),
                       covB=c("Class 1","Class 3","Class 2","Class 4","Class 4","Class 1","Class 1","Class 0"),
                       covC=c("Class 3","Class 3","Class 2","Class 3","Class 1","Class 4","Class 4","Class 4"))

temp_covars <- c("covA","covB","covC")

temp_locvec <- c(0.1,0.3,0.5,0.7,0.9)
temp_labvec <- c("0-1","1-3","3-7","7-10","10-15")
temp_colvec <- rainbow(n = 5,start = 7/12,end = 9/12,alpha = 0.8)

for(x in temp_covars) {

    cat(paste("## Spineplot of",x,"vs. age groups\n",sep=" "))

    spineplot(x = tempdata[[x]],
              y = tempdata$age,
              ylab = "Age Group",
              xlab = "Class",
              col = temp_colvec,
              off = 0,
              yaxlabels = c(NA,NA,NA,NA,NA),
              main = paste("Classes of",x,"versus age groups",sep=" "))

    for(j in 1:5) {
        axis(side = 2,
             at = temp_locvec[j],
             labels = temp_labvec[j],
             col.axis = temp_colvec[j],
             font.axis = 2)
        }
    rm(j)
    cat("\n\n")
}
rm(list=c("x","temp_locvec","temp_labvec","temp_colvec"))
```

Answer 2

I paste a short example I had prepared for another question:

```{r, results='asis'}
cat("\n\n## Title")
for (s in unique(cars$speed)){
    cat("\n\n### speed",s)
}
```

I deleted that example in the other question as it was on markdown syntax and didn't fit with Latex/ Rnw topic.