Report Design

[mbcole]

For Interactive: Sliders and interactive menus

• [x] Select Normalization (Non-interactive is single-normalization)
• [x] Select k for PAM (Best)
• [x] Color code by bio, batch, or PAM labels (for PCA plots)

Main Panel

• [x] PCA - Full PCA, Control Genes (Decide later on gene filtering)
• [x] Correlation with Quality and QPCA colored by whatever (init pam)
• [x] Silhouette - Bar-plot with silhouette width per sample by any of the three categories. PAM clustered by bio by batch: three tables.
• [x] Control Genes - Heatmap per control gene set, colored by all three categories, ordered by PAM silhouette.
• [x] Stratification: Box-plots of PCs from tab 1 stratified by any of the three categories. Violin-plots or box-plots.
• [x] RLE: Plot bxp function

Export PAM Labels: Are you sure?

[mbcole]

Base implementation in d8705584911ade36baa84193e05e27be665dfc25