ByrumLab
commented
2 years ago If we can make a plot object with more control over labels and plot features, this would be ideal. Sometimes users will request certain molecules be labeled in volcano plots or various color changes. It would be nice to have the functionality to easily change the significance thresholds and other plotting features.
There is probably a better visualization plot we can add for proteiNorm to display the data distribution, mean, and variance to indicate how normalization accounts for technical variability and the data distributions. Need to look into this further.
Some also request heatmaps, which is not a standard output, but can be generated upon request. I currently use complexHeatmap for this using a certain significance threshold to provide the smaller list of molecules to plot.
clw09
Now that I've added ggplot as a dependency for the static DE plots, might be worth it to re-do some of the other plots in ggplot objects. Would also have the advantage of simplifying and re-leveling all the plotting functions to operate in the same way (making a plot object), and allow us to separate out the plot making and plot saving functionality.