Review UI

[nsheff]

Some minor suggestions for improvements to the user experience

• when plotting a single profile, it says "sample type: All Samples" on the ggplot from plotMIRAProfiles, which doesn't make sense
• sampleType appears to be a hard-coded column in plotMIRAProfiles, but it could be a parameter.
• I would like to be able to change the y axis of plotMIRAProfiles plots. you can do this easily with MIRA::plotMIRAProfiles(agMethCombined) + ylim(60,90) (maybe add this to vignette)
• featID option to plotMIRAProfiles does not make sense to me. change docs?
• user should not need to interface directly with the scoreDip function; we should hide this behind some other function. this simplifies syntax for users unfamiliar with data.table
• scoreDip uses binCount while aggregateMethyl uses binNum. standardize names. And actually it's not clear to me why both of these functions would require this parameter; shouldn't setting it once be enough? are they different? I think scoreDip can lose the parameter.
• can this be quieter? applying aggregateMethyl yields this output:

seqnames column name set to: chr
seqnames column name set to: chr
seqnames column name set to: chr
seqnames column name set to: chr
seqnames column name set to: chr
seqnames column name set to: chr
seqnames column name set to: chr
seqnames column name set to: chr
seqnames column name set to: chr
...

[nsheff]

🎗️ can we resolve this issue? have all of these points been addressed?