MetaProViz::Preprocessing QC plots

[ChristinaSchmidt1]

After some discussions I think we should consider to add some more QC plots:

1. RLA plot before and after normalisation (of course if no normalisation =TIC is done, than just the standard plot)
2. Additional PCA plot with pool samples and/or blank samples (if CoRE=TRUE).

[dprymidis]

Added PCA for pool samples in the Pool_Estimation function

If all data are used as input:

If Only pool samples were used

PCA for CoRe Media samples in already in there.

For the RLA, I am not sure if what I did is correct ( based on this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544854/, I did the following) :

1. log transform the data
2. got the median for each sample
3. subtracted the median from all the values for each sample.
4. make boxplots for each sample
5. Put boxplots (before and after norm) together

[ChristinaSchmidt1]

Great, thanks!

Yes, I think this is exactly how an RLA-ploy is done. If the user has provided conditions we can colour code the boxplots for conditions (no need for a legend of this thow).

FYI: There is another issue I opened where I posted about QC plots for Pool_Estimation, where I added two additional plots we could use as well.

[dprymidis]

This is done

[ChristinaSchmidt1]

I am just going trought he open issues and I think this one is complete (?). If yes, could you confirm and close the issue?