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DavisLaboratory / singscore

An R/Bioconductor package that implements a single-sample molecular phenotyping approach
https://davislaboratory.github.io/singscore/
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annot argument issues in plotDispersion #8

Closed annaquaglieri16 closed 5 years ago

annaquaglieri16 commented 5 years ago

Hi there,

it looks like when you try to run the function:

plotDispersion(scoredf,annot = factor(samples$Outcome),isInteractive = FALSE)

the input for annot should be a vector external from scoredf.

When running something like this:

plotDispersion(scoredf,annot = factor(scoredf$Outcome),isInteractive = FALSE)

after merging scoredf with sample's annotations, then the points are coloured by the first available column of scoredf in alphabetical order.

Cheers,

Anna

bhuvad commented 5 years ago

Hi Anna,

I have just made an update to the github version of the package that now allows multiple ways to specify your annotations. Annotations can be either discrete (factors and characters) or continous (numerics).

The annot argument can be used to pass the vector containing annotations as before. Additionally, annotations can be appended to the scoredf as a column and only column name alone can be specified as below:

scoredf$Outcome = samples$Outcome plotDispersion(scoredf, annot = 'Outcome', isInteractive = FALSE)

In case you choose to use an independent vector containing the annotations of interest, the plotting functions now allow the annot_name argument which allows you to label the legend.

We will be pushing these changes as an official update for the package when possible soon. Feel free to use the version on github in the mean time and help us idendify any more improvements/bugs.

Cheers, Dharmesh Bhuva