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Multiplot Studio v1.5.29


This is a complete replacement for Multiplot. It has been completely rewritten from the ground up. See preview documentation for further description.

Some key improvements/additions vs the original Multiplot:

  • Direct reading of GCTs (no need for MultiplotPreprocces).
  • Major reduction in memory requirements.
  • Save/Load entire workspace.
  • Up to 4 plots at once.
  • Independently resizable plot windows
  • User can specify exact resolution of copied/exported images.
  • Export to SVG format for publication quality plots.
  • Alternate display formats for fold change values (e.g. as percentages, log2 fc, ±symmetric, etc.)
  • New calculations (std dev, variance, delta factor, ANOVA).
  • Additional scope options for existing calculations.
  • Option to plot rank of a calculated value instead of the value itself.
  • Improved GUI - much more efficient use of screen space.
  • Multiple data selection modes (elliptical, freehand, polygon).
  • Improved tooltips for mouseover of data points.
  • Quick search by probeID or gene symbol.
  • Create highlights/filters from lists of gene symbols.
  • Batch creation of highlights by dragging multiple TXT files (containing probeIDs or gene symbols, 1 per line) onto workspace.
  • Add probeID/gene symbol annotations directly to plots (move by drag-n-drop, customize appearance).
  • Add fold change guide lines to any plot containing FC or d-factor values.
  • On-the-fly calculation distributions making it easier to find appropriate thresholds for filters/highlights.
  • Heatmap for selected subset of data points.
  • Edit filters/highlight criteria without having to remove/re-add them.
  • Clone filters/highlights.
  • Per-plot activation of filters/highlights (apply to all plots, or only some).
  • Reorder highlights to determine which points appear on top (for highlights that contain overlapping items).
  • Advanced shading options for data points - color points according the intensity of some calculation (or by density).

Known Issues:

  • Polygon mouse selection acts a little strange at times (temporarily disabled until resolved).

Your feedback is greatly appreciated.

NOTE: This module can also be run as a stand-alone Java desktop app by extracting the ZIP file to a separate folder and double-clicking MultiplotStudio.jar.

- Scott Davis

 


REVISION HISTORY


1.5.29 - Oct 9, 2014

FIXED   Various bug fixes.


1.5.20 - July 8, 2014

FIXED   Several bugs related to the data browser/heatmap.
FIXED   IDs with commas and spaces can now be used in ID-based filters/highlights.
FIXED   Update density calculation to be based on only those probes that are currently visible after applying all active filters.
FIXED   Various bugs/glitches related to creation and editing of highlights/filters.
ADDED   Added histogram plot to highlight/filter editor.
ADDED   Export (copy/save) rank & histogram distribution plots via right-click.
ADDED   Summary of number of missing values for a given calculation criterion in highlight editor.
ADDED   Export current data from heatmap to CSV.
ADDED   Some additional calculation scopes.
MOD     General performance optimizations.
MOD     A bunch of other stuff.

 

Language:
Java
Operating System:
any
Original Author:
Scott Davis (Tempero Pharmaceuticals)
Uploaded by:
sdavis on July 02, 2015 07:58
Version Comment:
Completely rewritten and vastly improved replacement for Multiplot