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examples of how to make PCA and/or NMDS? #932

Closed grace-ac closed 4 years ago

grace-ac commented 4 years ago

Assigning everyone, because I'm not sure who all has made these kinds of plots...

I have gene expression data from individual crabs across time and want to make a figure of relatedness.

Any examples from your own work of how to make a PCA and/or NMDS?

yaaminiv commented 4 years ago

NMDS code: https://github.com/RobertsLab/paper-gigas-DNR-proteomics/blob/master/analyses/7-SRM/2018-02-15-DNR-Paper-Figure/2018-02-15-DNR-Paper-Figure.R PCA code: https://github.com/epigeneticstoocean/paper-gonad-meth/blob/master/code/04-methylkit.Rmd

Can also send code from the multivariate class!

laurahspencer commented 4 years ago

I've used the DESeq2 tutorial to compare expression by groups, and it includes some PCA plots which can be customized via ggplot tools: http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

From Julian's Multivariate class, here are materials related to PCA (and NMDS, PCoA). I think i've included all the data files needed to follow the tutorials - if you're missing something important let me know!: PCA-materials.zip