Panels for a tumor purity figure, part 1

[sjspielman]

Towards #1665

This PR updates three modules, including code and docs, to export plots that can be used towards the tumor purity SI figure. As proposed in #1665, these are (with nested bullets indicating relevant changed files) -

• Panel A distribution of tumor purity by cancer group: analyses/tumor-purity-exploration/plots/cancer_group_tumor_fraction.pdf

  • analyses/tumor-purity-exploration/01_explore-tumor-purity.Rmd and html
  • analyses/tumor-purity-exploration/README.md

• Panel D remake UMAP with high purity tumors only: analyses/transcriptomic-dimension-reduction/plots/umap_tumor-purity-threshold.pdf

  • analyses/transcriptomic-dimension-reduction/analyses/transcriptomic-dimension-reduction/06-umap-tumor-purity-threshold.Rmd and html
  • analyses/transcriptomic-dimension-reduction/README.md

• Panel E quanTIseq estimations of immune fractions across cancer groups: analyses/immune-deconv/plots/tumor-purity-threshold_quantiseq-cancer-groups.pdf

  • analyses/immune-deconv/03-quantiseq-at-threshold.Rmd and html
  • analyses/immune-deconv/README.md

[jharenza]

I think it would be nice to add Panel A to the manuscript, and the remaining panels (along with A as the multi-panel figure @jaclyn-taroni suggested) to the reviewer response. Can we add this as Supp Figure 3A, perhaps splitting the space with the oncoprint, making that B and so on?