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sr320 / ceabigr

Workshop on genomic data integration with a emphasis on epigenetic data (FHL 2022)
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PCAs of methylation and gene exp data #73

Open yaaminiv opened 1 year ago

yaaminiv commented 1 year ago

@kubu4 @sr320 Where can I find the PCAs of methylation and gene exp data? Looking for sex-specific PCAs ideally, but would take PCAs of all data

kubu4 commented 1 year ago

Like in this Mixomics "testing" I ran through?

https://rpubs.com/kubu4/cvir-gonad-oa-mixomics_testing

yaaminiv commented 1 year ago

@kubu4 yes! is there any way you could color the PCAs by sex and treatment? those would work great

kubu4 commented 1 year ago

is there any way you could color the PCAs by sex and treatment

Can you clarify exactly what you have in mind?

On those plots, they're colored by sex and then shapes designate treatment.

Are you wanting four colors? Do you want the shapes to remain?

And, after all those questions, I honestly have no idea if I can figure that out! LOL! I just followed the Mixomics tutorial, so would have to dig much deeper to see if I can figure out other ways to manipulate the plots....

kubu4 commented 1 year ago

Also, just to note, gene expression and methylation are only taken into account for the sparse Projection to Latent Structure (sPLS), not in the PCAs.

sPLS tutorial I followed is here:

https://mixomicsteam.github.io/Bookdown/pls.html

yaaminiv commented 1 year ago

On those plots, they're colored by sex and then shapes designate treatment.

ah never mind! i didn't see the different shapes