r - export data frames to Excel via xlsx with conditional formatting

Question

I want to export data frames to Excel and highlight cells according to certain rules. I don't think this answer to a similar question is correct. I think it is possible, and I think I get close using the CellStyle functions of the xlsx package.

Below I outline what I've tried. Most of the ideas come from the package help files. I get all the way to the end and get an error when I try to apply the style I created to the cells that meet the criteria. I get the error: Error in .jcall(cell, "V", "setCellStyle", cellStyle$ref) : RcallMethod: invalid object parameter.

library(xlsx)
# create data 
  cols <- sample(c(1:5), 1) # number of columns to vary to mimic this unknown
  label <- rep(paste0("label ", seq(from=1, to=10)))
  mydata <- data.frame(label)
  for (i in 1:cols) {
    mydata[,i+1] <- sample(c(1:10), 10)
  }
# exporting data.frame to excel is easy with xlsx package
  sheetname <- "mysheet"
  write.xlsx(mydata, "mydata.xlsx", sheetName=sheetname)
  file <- "mydata.xlsx"
# but we want to highlight cells if value greater than or equal to 5
  wb <- loadWorkbook(file)              # load workbook
  fo <- Fill(backgroundColor="yellow")  # create fill object
  cs <- CellStyle(wb, fill=fo)          # create cell style
  sheets <- getSheets(wb)               # get all sheets
  sheet <- sheets[[sheetname]]          # get specific sheet
  rows <- getRows(sheet)                # get rows
  cells <- getCells(rows)               # get cells
  values <- lapply(cells, getCellValue) # extract the values
# find cells meeting conditional criteria 
  highlight <- "test"
  for (i in names(values)) {
    x <- as.numeric(values[i])
    if (x>=5 & !is.na(x)) {
      highlight <- c(highlight, i)
    }    
  }
  highlight <- highlight[-1]
# apply style to cells that meet criteria
  if (length(highlight)>0) {            # proceed if any cells meet criteria
    setCellStyle(cells[highlight], cs)  # DOES NOT WORK
  }
# save
  saveWorkbook(wb, file)

Update: I've also tried:

if (length(highlight)>0) {                # proceed if any cells meet criteria
    for (h in 1:length(highlight)) {
      setCellStyle(cells[highlight[h]], cs)  # DOES NOT WORK
    }
  }

But I get the error: Error in .jcall(cell, "V", "setCellStyle", cellStyle$ref) : RcallMethod: cannot determine object class

Answer 1

Try this out. I changed a few things, including the a slight change to the call to Fill and limiting the cells included for consideration to those with numeric data. I used lapply to apply the conditional formatting.

  cols <- sample(c(1:5), 1) # number of columns to vary to mimic this unknown
  label <- rep(paste0("label ", seq(from=1, to=10)))
  mydata <- data.frame(label)
  for (i in 1:cols) {
    mydata[,i+1] <- sample(c(1:10), 10)
  }
# exporting data.frame to excel is easy with xlsx package
  sheetname <- "mysheet"
  write.xlsx(mydata, "mydata.xlsx", sheetName=sheetname)
  file <- "mydata.xlsx"
# but we want to highlight cells if value greater than or equal to 5
  wb <- loadWorkbook(file)              # load workbook
  fo <- Fill(foregroundColor="yellow")  # create fill object
  cs <- CellStyle(wb, fill=fo)          # create cell style
  sheets <- getSheets(wb)               # get all sheets
  sheet <- sheets[[sheetname]]          # get specific sheet
  rows <- getRows(sheet, rowIndex=2:(nrow(mydata)+1)     # get rows
                                                         # 1st row is headers
  cells <- getCells(rows, colIndex = 3:(cols+3))       # get cells
# in the wb I import with loadWorkbook, numeric data starts in column 3
# and the first two columns are row number and label number

  values <- lapply(cells, getCellValue) # extract the values

# find cells meeting conditional criteria 
  highlight <- "test"
  for (i in names(values)) {
    x <- as.numeric(values[i])
    if (x>=5 & !is.na(x)) {
      highlight <- c(highlight, i)
    }    
  }
  highlight <- highlight[-1]

lapply(names(cells[highlight]),
       function(ii)setCellStyle(cells[[ii]],cs))

saveWorkbook(wb, file)