create UpSet plot

[shellywanamaker]

Pact draft 1:

ALL = all CpGs in the genome WGBS = compiled CpGs detected in WGBS samples RRBS = compiled CpGs detected in RRBS samples MBD = compiled CpGs detected in MBD samples *CpGs could be detected in just one sample or in multiple samples ( I merged sample bedgraphs using bedtools merge for each method)

Rmarkdown script here: https://github.com/hputnam/Meth_Compare/tree/master/analyses/UpsetPlot

still need to:

• QC merged bedgraphs
• QC union bedgraph
• do this for Mcap

[shellywanamaker]

Included Mcap in the analysis and all QC of merged bedgraphs and union bedgraphs were good. This is noted in this jupyter notebook: https://github.com/hputnam/Meth_Compare/blob/master/scripts/Generate_UpsetPlot_input.ipynb.

Pact:

Mcap:

[shellywanamaker]

Updated Pact upset plot with annotations

[shellywanamaker]

Updated plots so label text isn't cutoff

a. Pact b. Mcap

[shellywanamaker]