Heatmap & Composite Styling

Heatmap checklist

Use ScriptManager's heatmap labeler for convenient and bulk-style labeling of heatmaps with the following info

• PNG is bordered
• x-axis label
  • axis label (RefPT) for feature being aligned to (peaks, motifs, annnotations)
  • include range labels for the left-bound, mid bound, and right-bound limits (e.g. -500, 0, +500)
  • Example: Reb1 motif (bp) ⚫ -500, 0, +500
  • Example: Sua7 peak (Kb) ⚫ -1, 0, +1
• y-axis label
  • axis label (info on filters, groups, sort, and include n sites)
  • Example: Sort by Reb1 Occupancy (500 sites)
  • Example: Sort by Gene Expression (5,378 genes)
• Title
  • per-dataset descriptive title for signal being plotted (include PEGR id for lab presentations)
  • Example: Reb1 ChIP-exo (12141)
  • Example: Sua7 PIP-seq (28576)

Composite checklist

Use plotter to create SVG-style composite figures for presentations and publications. Don't forget to save it as JSON too for your records!

• legend: label datasets with descriptive names to show which color indicates which
• title
• x-axis: axis label (RefPT) and range (left, mid, and right bounds)
• y-axis: axis label (units, usually "AU" for "Arbitrary units"/"Abstract units") and range
  • range is automatically taken care of if you use plotter
  • A common label is Occupancy (AU)
• n sites (N=XXXXX) summarized by composite
  • i.e. how many BED coordinates are these composites averaging from (lines in BED file)
• normalization label
  • indicate normalization strategy used (NCIS, Total Tag, NFR strategy)
• IgG if appropriate (if not sure, just include it)
• check for optimal layer order
  • make sure composites aren't hiding behind each other so you can see them all