shiny 2

[yuhanhsu]

Basic Plots

• [x] default enrichment thresholds: FDR <= 0.1 and logFC > 0
• [ ] adjust horizontal dashed line to show FDR cutoff? (or just don't show horizontal line when using FDR cutoff)
• [x] scatterplot naming (e.g. "rep1 vs. rep3")
• [x] color selection dropdown menu: show actual colors in a matrix
• [x] basic plot options: add abs(logFC) labels above color selection boxes (put boxes on two separate rows if need more space)
• [x] summary box: spell out what numbers mean (e.g. "91 out of 556 proteins enriched")
• [x] move basic overlay (protein family removal) to "Protein Family" tab
• [x] download buttons for: volcano plot, scatter plot, moderated t-test results table

Integrated Plots

• [x] options for each overlay dataset: (1) label on/off, (2) color selection (make consistent with color selection in Basic Plots), and maybe (3) shape selection
• [x] add/modify get_snp_list, get_gene_list, get_gwas_list functions to allow multiple input lists (as separate columns). Return df with additional listName column (so listName can be labeled in volcano plot)
• [x] GWAS catalog: allow selection of multiple traits
• [x] order: InWeb, GWAS catalog, SNP, gene
• [x] download buttons for: overlaid volcano plot, summary table of overlaid genes (and which list they came from) + relevant overlap enrichment statistics