refactor: convert section "definPlotParams" into functions

[sof202]

Description

This pull request:

• Forcibly stops the creation of the QCmetrics report if columns are not identical between the config file and the sampleSheet.csv. The error message is now also updated such that it provides the necessary information to fix the issue in the error logs.
• Correctly identifies columns that should not be brought forward into the later plots
  • Which include:
  • Columns with all missing values
  • Columns with only a single unique value (contrasts() will fail in this case)
  • Columns that contain all unique values (not sure why this is the case, but the old code did this)
• Refactors the definPlotParams section to use functions and less repeated code

Issue ticket number

This pull request is to address issues: #173 and #177.

Type of pull request

• [x] Bug fix
• [ ] New feature/enhancement
• [x] Code refactor
• [ ] Documentation update

Checklist

• [x] I have performed a self-review of my own code
• [x] I have commented my code, particularly in hard-to-understand areas
• [ ] I have tested my code to check that it is functional
• [x] I have used linters to check for common sources of errors
• [x] I have implemented fail safes in my code to account for edge cases
• [ ] I have made the corresponding changes to the documentation

[sof202]

Current problems with my code

One

If both techVar and bioVar are undefined, then plotCols will just be the Basename column of QCmetrics. Is this the desired effect? (This is what the code did before, just checking if this is actually what we want.)

Two

Not sure if I like the if statement hell:

if (all(is.na(column))) return(FALSE)
if (length(unique(column)) == 1L) return(FALSE)
if (anyDuplicated(column) == 0L) return(FALSE)
return(TRUE)

I could change this to:

if (
all(is.na(column)) || 
length(unique(column)) == 1L || 
anyDuplicated(column) == 0L) {
  return(FALSE)
} 
return(TRUE)

Or:

return(!(all(is.na(column)) || 
          length(unique(column)) == 1L || 
          anyDuplicated(column) == 0L))

Though I'm not convinced these are much cleaner. I'm open to suggestions

[sof202]

Not sure if I like the if statement hell:

if (all(is.na(column))) return(FALSE)
if (length(unique(column)) == 1L) return(FALSE)
if (anyDuplicated(column) == 0L) return(FALSE)
return(TRUE)

I could change this to:

if (
all(is.na(column)) || 
length(unique(column)) == 1L || 
anyDuplicated(column) == 0L) {
  return(FALSE)
} 
return(TRUE)

Or:

return(!(all(is.na(column)) || 
          length(unique(column)) == 1L || 
          anyDuplicated(column) == 0L))

Though I'm not convinced these are much cleaner. I'm open to suggestions

I've chosen the 3rd option now