Color Coding Sweave Only Partially Working

Question

I am still working on this question. I've got it so it gives the correct cells red backgrounds, but it is not giving the other cells green backgrounds.

Note: I am using sweave only, not knitr.

Here is my code:

<<>>=
Flag <- data.frame(HOSP,Dept, Overall, DC_Info, Care_Trans)
@  
<<results=tex>>=
color_cells <- function(df, var){
  out <- ifelse(df[, var]=="", 
                  paste0("\\cellcolor[HTML]{2DB200}{", df[, var], "}"),
                  paste0("\\cellcolor[HTML]{FF0600}{", df[, var], "}"))
}
Flag$Overall <- color_cells(df = Flag, var= "Overall")
Flag$DC_Info <- color_cells(df = Flag, var= "DC_Info")
Flag$Care_Trans <- color_cells(df = Flag, var= "Care_Trans")
@

<<results=tex>>=
Flagx <- xtable(Flag)
align(Flagx) <- "|c|l|l|c|c|c|"
print(Flagx[1:40,], hline.after=c(-1:40), sanitize.text.function=identity,
sanitize.colnames.function = Hmisc::latexTranslate)
@

Answer 1

A couple of things that may be contributing:

This is subtle and I've missed it even in the earlier questions. In your color_cells function, you are assigning a character string to out, but you aren't returning the value of out. You should write your function in one of the two following ways:

color_cells <- function(df, var){
  ifelse(df[, var]=="", 
         paste0("\\cellcolor[HTML]{2DB200}{", df[, var], "}"),
         paste0("\\cellcolor[HTML]{FF0600}{", df[, var], "}"))
}

OR

color_cells <- function(df, var){
  out <- ifelse(df[, var]=="", 
                paste0("\\cellcolor[HTML]{2DB200}{", df[, var], "}"),
                paste0("\\cellcolor[HTML]{FF0600}{", df[, var], "}"))
  out
}

Another issue that may be contributing (though I'm not entirely sure in this case) is whether your columns have any NA values. Watch what happens if a value is NA: The logical comparison doesn't resolve and returns NA without applying any color.

> ifelse(NA == "", "red", "green")
[1] NA

You can modify your cell_colors function to handle theNA`'s with something like

color_cells <- function(df, var){
 df[, var][is.na(df[, var])] <- ""
 ifelse(df[, var]=="", 
        paste0("\\cellcolor[HTML]{2DB200}{", df[, var], "}"),
        paste0("\\cellcolor[HTML]{FF0600}{", df[, var], "}"))
}