Report Design
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mbcole commented
For Interactive: Sliders and interactive menus
- Select Normalization (Non-interactive is single-normalization)
- Select k for PAM (Best)
- Color code by bio, batch, or PAM labels (for PCA plots)
Main Panel
- PCA - Full PCA, Control Genes (Decide later on gene filtering)
- Correlation with Quality and QPCA colored by whatever (init pam)
- Silhouette - Bar-plot with silhouette width per sample by any of the three categories. PAM clustered by bio by batch: three tables.
- Control Genes - Heatmap per control gene set, colored by all three categories, ordered by PAM silhouette.
- Stratification: Box-plots of PCs from tab 1 stratified by any of the three categories. Violin-plots or box-plots.
- RLE: Plot bxp function
Export PAM Labels: Are you sure?