Coulson Plot Generator Files

============================

Coulson Plot Generator (CPG)

============================
Release 1.6 (v1.6.2)
============================

Last updated 2014-08-15 by H.I.Field
CPG copyright Helen Field 2009-2050


CONTENTS:

Disclaimer and license.
Copyright
System requirements
CPG Description
Input data formatting
How to use CPG
BUG fixes and updates
Contact.


ACCOMPANYING DOCUMENTS:
xalanLICENSE.txt
CPG_LICENSE.txt

ALSO Note that this software is now bundled with Apache xalan-j in order to provide svg output, so is also accompanied by the Apache licences.

This software is written in java and packaged as a Mac application.
It is subject to the Artistic License 2.0, or as previously released:

============================

Coulson Plot Generator (CPG)

============================
Release 1.6 (Development v1.6.2)
============================

Artistic License 2.0
=====================
Artistic License 2.0
Copyright (c) 2000-2006, The Perl Foundation.

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

Preamble
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+++++++++
COPYRIGHT
=========

CPG software copyright Helen Field 2009-2050

==========
DISCLAIMER
==========

Disclaimer: no responsibility is taken for use or development of this software.


================================
TESTING and Systems requirements
================================
Software was developed for Mac
However, it is pure java and is in theory be compiled for any OS.
It is actually compiled on a Mac for Java 1.6 using Eclipse Indigo Build id: 20110615-0604
New versions tested on Mac Mavericks, Windows 7 (in Virtual Box).

Previous versions tested on Mac OSX versions 10.6.8 (Snow Leopard) and 10.7.2 (Lion) and 10.8.x (Mountain Lion)
Linux RedHat RHEN5, Ubuntu, Solaris 11g
Windows 7, 2008, Server 2003.

Memory requirements: 
---------------------
For proper rendering of saved images at least 1 GB RAM is required: -Xmx2G -XX:MaxPermSize=512M

In the Mac app these settings are automatically applied. 
If running the jar file alone these may be entered on command line or the cpg.sh used (below).

USING THE DOWNLOADS:
---------------------
Test input data and a sample color file are provided with the Download.

To use on MAC:

The installer places the Application in your /Applications folder
together with a folder containing the test data.
Navigate to your personal Applications folder, and into the folder CPG.
Double click on the CPG icon.

To use on LINUX (command line):

Ensure that the .cpg, and Resources folders are present alongside the jar file, by entering on the command line*:
> ls -la

To run from the command line enter these two commands:
> cd WinLin/CPG
> java -Xmx2G -XX:MaxPermSize=512M -jar CPG.jar

OR use the shell script*:
> cd WinLin/CPG
> sh CPG.sh 

An alternative to the latter command:
> ./CPG.sh

* You can try increasing the -Xmx and -XX:MaxPermSize parameters for java memory.


To use on WINDOWS:

The application is provided for Windows as a double-clickable jar file.

Unpack the WinLin.zip folder (by double clicking on it).
Put the WinLin folder into a convenient location (anywhere).
In Windows Explorer, navigate to the folder WinLin/CPG and 
double click on CPG.jar. 
IMPORTANT: do not remove CPG.jar from its location inside the its parent folder or it will not work.
Keep the whole WinLin folder intact: the README_CPG and Resources folder must be present alongside the jar file.



====================
CPG Description 
====================

The Coulson Plot Generator (CPG) provides a visual comparison of entities, as an array of pie diagrams in rows and columns,
with headings (3-4) for phylogeny and unit/subunit labels to identify pie wedges:
		 X 	Y
		abc	d
		
	1	ooo	o
	2	ooo	o
	3	ooo	o
		
The diagram is labeled and may resized, recolored, transposed and then exported in various image file formats,
including svg, for touch up in a PDF or drawing editor such as GIMP.

Each pie represents an entity which is divided into subcomponents (wedges).
Each pie can represent a component whose subcomponents (genes, traits or other fac-tors) are present or absent (shown as filled or empty pie slices, respectively)
 in different entities (e.g. species).

The input is a .csv (comma or tab separated) text file, which governs
- the number of pies per row 
- the number of pies in each column
- the number of wedges per pie (can differ for each pie type)
- the labels and sublabels (2-3 additional headers) for rows (contained in the top 4 rows heading each column)
- the pie labels, wedge labels, and the number of  wedges per pie (contained in the first 2 columns)
- presence or absence of a subcomponent (denoted by + or - representing presence and absence. Alternatively, 1 and 0 may be used)

CPG creates a set of pie diagrams from a .csv file containing four column headings (4), and two row labels (2). 
See accompanying document (pies.jpeg) for an example of the output graphic, and the Coulson_Plot.csv input file for an actual input.

======================
Input data formatting:
======================

Generate an input file containing your data, in a table editor that can generate tab or comma separated output.
Input is a text file (tab or comma separated) containing a table of pie wedges (use + or 1 to fill, - or 0 for empty).
PLEASE see the examples in TestData, opened in a spreadsheet application, before creating your own data.

In the input file there are 4 lines of headers, describing e.g. 
-Phylum (row 1) 
-Kingdom (row 2)
-SPECIES (row 3) - the main header in the plot, labelling each row/column of pies: there must be one SPECIES heading for every row/column
-other info (row 4, optional) - as for row 3, one heading for each item
Put nothing into the first two cells/columns: these columns are used to describe the pies.

The pies and wedges are described in Columns 1 and 2 (put nothing into the header rows):
The pie title appears in column 1 and the pie wedge names in column 2:
- in Column 1, the pie name must be placed once, at the top of the list of pie wedges alongside the first pie wedge name in Column 2 
- in Column 2, *every* pie wedge has a title/entry

Data
- in other columns the wedge occupancy data is placed, using +/- or 1/0 for filled/empty wedges.Use the same system throughout.


See the INPUT examples for details:
- pie.txt is an example of multi-wedged pies
- dot.csv is an example used for a dot plot


IMPORTANT: data appears transposed in the default figure, compared to the layout in the input file. However, the figure may be transposed by CPG.
- row 3  i used for your headers (species) and these will appear on the left as pie ROW labels.
- the first two COLUMNS contain the names of the pie entities (column 1) with subcomponent names (column 2) and appear across the top of the graphic
	as entity names, and a labeled pie. 

To trouble shoot data inputs, please review the output messages in the log file, or review your file in a spreadsheet editor.
The log messages are available in the Log tab, in the first CPG window: to see it, select 'Show Log' in the Preferences (and then restart).

A Log, available in the first window as a fourth tab (set using Preferences) 
  gives you information on file formatting and data processing. 
  
If input data is unacceptable (because it has one or two headers) the Figure button is inactivated;
  also the data may not appear to be inserted into the table (second window).
  Informative messages appear in the Log (first window), 
  and important messages also appear in Console output (system log). 

INPUT examples (pie.txt, dot.csv)

==============================
Using CPG to generate figures:
==============================

Open the application (above). 
In the first window with 4 tabs, use 'Open Data File' to select the input file.

To choose your own colors, or return to the default (hard coded) selection,
use the Color tab in the first window. 
A Color picker is available for creating a file of colors: if only a few are selected then they are iterated in the final diagram.

The third tab contains the Help message (this document).

The fourth tab (optional) contains the Log; this may be hidden (use Preferences to deselect 'Show Log' and then restart CPG). The log is used to help sort out any formatting issues with input data.

INPUT DATA FILES
Data input files must be prepared 'by hand', as a spreadsheet.
Please review the accompanying test data file examples, 
preferably in a spreadsheet application to ensure that no cell has been mis-placed,
and perhaps in a text editor,
 and ensure the following rules apply to your own dataset:
- text file
- tab or comma separated (allowing spaces to appear in headers)
- 3-4 header rows across the top (labels e.g. taxa) and 2 heading columns down the left hand side (pies e.g. protein complexes)
- 3-4 header rows with (first 2 items empty)
- 3rd row headers must ALL be filled in, other than the first 2 cells, (and each will have a complete data set in the rows below it)
- 4th row headers are optional and the entire row may be omitted
- 2 'header' columns (top rows empty)
	- column 1 only populated at the start of a 'pie'
        - column 2 labels every segment
  Note that for a dot blot every 'header' column 1 row has a value/label in column 1 (and also in column 2)
- body of table populated with either + and - or 0 and 1
- a completely empty line between data rows is allowed


After selecting an input file, a table window appears.
If the input is correct then the data appears in the table: if it does not appear correctly, open the data in Excel to check it, and see the Log tab in the main CPG window.
The table will omit headers above the header line on Row 3, which should read as text labels: 
Although you cannot see Row1 and Row2 (and Row4) headings they will appear on your figure.
If you have a fourth row of headers these labels appear alongside those from Row3 but only in the figure. 

If the figure button is not active, please review the Log (fourth tab in first window) to detect problems with the input data.

You may use the 'Open Data File' button to open several table views on different input files.

From the table window, you can generate a Coulson Plots, many times with variations.
Use 'Figure' to generate a plot.
Each time you may wish to test some parameters e.g. font or pie size. 
If any item is out of range it is automatically corrected.

In the CPG diagram window, you may Save the picture as a PDF (using Print and save as PDF) or other image format (using Save...).
Use a very large JPEG for good resolution, or use SVG, and when opening it in a picture editor (such as GIMP) choose a very large size for rendering your image
e.g. 10x the original suggestions for pixels.
You may change the sizes of the pies and the space they occupy.
You may change the spacing of the groups (coloured) and subgroups (same colour but with spaces in between).

For a large diagram, you can increase the number of pies per page by:
- reducing the size of individual pies (Row height, Pie diameter) and the font size
- increasing the size of the view window containing the Coulson Plot diagram
- for non-editable images, decrease the scale: NOTE - increase the scale for better resolution 
- NOTE for printing to an editable PDF, you must see all the pies in the window, 
  and use Page set up to create a printout of the correct size and orientation
  (there is no warning about clipping).
- simply use Fit to window (Cmd-F) to put all the pies into the CPG plot window. There are zoom tools to zoom in and out (Cmd= and Cmd-).
	From Release 1.1 there is a zoom facility, and a Fit to window function where
 CPG will attempt to resize the drawing for the current window size. 
	
 
DO center the image in the view window, in order to avoid white space in your PDF: 
for a small plot this may mean starting with a small window.

Use the zoom in/out to create the view that you need: this zooming will not affect the final output drawing size

In Preferences you can set the application to quit without asking (implemented without restarting the program).

The output (PDF) is NOT camera ready: it is designed to be opened with a Scalable Vector Graphics  package
such as Adobe Illustrator or Inkscape, 
and edited: each element may be fully unmasked and reformatted, but not within CPG.
If you cannot see the complete label, then by opening the editable PDF and selecting the element, 
you can remove the clipping mask from any label, for its complete display.
In svg format you will see all of the text: SVG format may be rendered with GIMP.

For convenience, figures may be saved in several graphics formats including svg (which should be rendered with a high no. of pixels)
- for other formats, use large scale for better resolution. 
Page set up may also affect the output (amount of data that can be viewed per page).

When using Save... from the Plot window, to save non-editable images as jpg, jpeg, bmp, wbmp, png, svg etc,
the scale can be decreased to fit more into a page, or increased for a high resolution image (and shrunk later for printing).
After selecting the output image format, use the 'Save as' button for the File dialog choosing the output file location/name.

---------------------
UPDATES and BUG FIXES
---------------------
Most recent first:


---------------------
Current Release 1.6 
on 15 August 2014 
---------------------

Development Version 1.6.2 --- 15 August 2014

New feature
	build.xml and jarbundler version included, for 1.6 (Java) compilation on Mavericks with Mac native JRE 
Bugs fixed: 
	Fixed bug causing misplotting (introduced in 1.6.1)
	Resize 'bug' - after resizing window the figure should remain the same size, except for the first resize 
	Upon resize, have removed the 'Fit to window' feature, which is now accessed as before via the menu, or Command-F	
Known issues
	1. The first time resize window happens the picture is not persistent - so resize again or perform a fit to window or zoom command 
	(Cmd-F, Cmd--, Cmd-=).
	2. Saved files in svg format may not open in Illustrator (Error is CANT) but may be rendered in GIMP
New Developer items
	build.xml and jarbuilder.jar to create CPG.app, for Apple running Java 1.6 (as installed, no extras), with instructions for developers.
	 
Development Version 1.6.1 --- 2 August 2014

New feature
	None
Bugs fixed: 
	CoulsonPlotPrintable added a missing top line of data when using 4 headers (correct if 3 headers).
	Link on About screen updated for University of Dundee (Mark Field)

Development Version 1.4.9 --- 19 March 2013

New features
     * Log tab SHOWN by default 1.4.5 (1.1 Patch 1)
     * Remove line from singleton 1.4.6 (1.1 Patch 2)
     * Add Save as button for saving image to file, and SVG save capability 1.4.7 (1.1 Patch 3)
     * Refresh problem: increased memory. Change Figure to Plot.. 1.4.8 (1.1 Patch 4)
     * Zoom on window resize working. Fit to window working. First plot left alone so blanks not so obvious. Zoom set to increase or decrease by 1/20 instead of 1/10 when resizing (1.1 Patch 5)

Bugs fixed: 
	Zoom on window resize working. Fit to window working. 
	First plot left alone so blanks not so obvious. 
	Zoom set to increase or decrease by 1/20 instead of 1/10 when resizing with Cmd- or Cmd=


Development Version 1.4.8 --- 18 March 2013

Bugs fixed: 
	Refresh in windows addressed. Increased memory (1G and 2G releases)

Known issue:
	When Coulson plot is first drawn after the initial plot the refresh removes the diagram until either the window or the diagram is resized (use Cmd- or Cmd=, or resize the picture).


Development Version 1.4.7 --- 9 March 2013

Bugs fixed: 
	Single spoke in a circle of one segment now removed.

New features: 
A. Log now shown by default, as fourth tab, to assist with data importing.

B. SVG graphic support is provided, so that images may be saved straight to svg.
This is accessed from the Coulson Plot image window, using File > Save... and choosing svg

SVG generation is provided by xalan-j (apache.org), which is included in the CPG application.

Xalan-j was downloaded as follows on 26 February 2013:
svn checkout http://svn.apache.org/repos/asf/xalan/java/trunk xalan
The apache licence is included as a separate document. 

To create the application a runnable jar file must be exported from Eclipse, with CPG_lib folder containing shared libraries. This can be packaged for Apple using the Jar bundler and putting .cpg, Resources and CPG_lib alongside the CPG.jar in CPG.app/Contents/Resources/Java/


---------------------
Release 1.1 
on 29 October 2012 
---------------------

Development Version 1.4.4.3 --- 24 Oct 2012

Bugs fixed: 
	slight misplacement of central protein labels in non-transposed mode. Grey square appearance.

New feature: 
A. Default path when first opened is that where Application, and TestData folder is found 
	ie in the application folder that one downloads. 

B. The last file picked is used as the next path and 
	*is now* remembered between sessions.


---------------------

Development Version 1.4.4.2 --- 22 Oct 2012

NEW features: 

A.    Figure can be readily enlarged and decreased using the
	- apple/Alt-minus to shrink and apple/Alt-equals to grow it: 
    	- size of the figure as viewed will not affect printing size.

B.    Window resize (in CPG plot window) results in a resizing of the CPG plot to fit the window.
    
C.    Table window remembers the last parameters used (e.g. transpose)

D.    All labels are colored along with the pies (except for the pie labels and pie titles)
	- same colors apply to boxes when drawn around label groupings
	NOTE: if a TOP line label is missing then groupings are not always correctly drawn.

E.    Text clipping occurs when the Coulson plot is first drawn. However
	AFTER resizing or zooming, all of the text is drawn full size. 
	Text boxes should be aligned correctly.

	Previously, in a Graphics editor, the masking clip had to be removed from the editable PDF.


    
KNOWN BUGS/ISSUES:

A. When first shrinking or resizing (fit to window) a large white rectangle may cover the drawing 	- use the Alt- or Alt=
	or resize the window (or fit to window) to recover the CPG plot.
    
B. Fit to window is an attempt to make the drawing fit the window
	- it is not perfect - if resize is not quite right use Alt-/Alt= to correct it.
	
C. When printing to PDF, there is no Warning if the picture will be clipped: 
	- use the print PREVIEW to check what you will get. 
   	- use **Page Setup** to make the print the correct size for the drawing:
	 an external editor can later be used to reduce the size. 
	 Larger printouts for the original PDF will improve resolution in the print quality.
    
---------------------
	

Development Version 1.4.4.1 --- 17 Oct 2012

NEW features: 
	For the figure:
	- when text is larger than the bounding label box, it is clipped in the original image.
	  Now when saved to PDF the text is unmasked (and the bounding box increased in size to surround the text)
	  While these overlap, they are more readily available for workup since the text is unmasked. --- v 1.4.4.1
	  This is true for layout of pies in either orientation (transpose)
	  
	- when transposed, pies are very close together, while the left outer (protein) labels and labelled pies have more space. --- v 1.4.4
	  In the untransposed view with pie labels on top, all the pies are double-spaced in order to give labelled pies sufficient space.
	
	- boxes for outer group labels are now outlined in the same color as the species text, and labels themselves
	  follow the same color scheme as the pies --- v 1.4.4

Bugs fixed: 
	Labels no longer jump around when saving to PDF --- v 1.4.4.
	When hiding then showing layout options in the Table window, items are no longer hidden.
	
KNOWN ISSUE (PLEASE READ):
1	When you choose to leave the color picker (Done) without saving the colors to file, and you are warned
	that you need to save, and Cancel - the color picker still quits. Remember to 'Save' colors to file first.

---------------------

Release 1.0
on 15 March 2012
---------------------


Development Version 0.9.4.2 --- 25 Feb 2012

NEW features: 
	For the figure: 
		Transpose option plots species across the top and protein/pie keys left (input is the same)
		Column gap may be specified. 
		Horizontal gaps may be for Row1, Row1 plus Row2 or no gaps at all.
		Yellow boxes may be drawn around groups for clarity (you may easily create another figure without them
	When you create a figure, if any settings are jigged because out of range you see this in the window.
	In Color Picker the color squares showing what you picked are a decent size  -- 20120206.
	Tiny bug manifesting as ClassCastException preventing restore localisation. -- v0.9.4.1

Bug fixed: 
	In figure, spacing of outer, vertical labels (Row1 and Row2 of input data)
	If ask before quit not required, program just quits (apple-q)
	In colors tab the default colors are properly restored.
	Can use Colors menu item when available (apple-k)
	
Pre release Version 1.1 Dev 0.9.2 -- 4 Jan 2012

New features: Preferences contains:
	 option to see the Log (4th tab in first window), 
	 option to ask before quitting.

Known BUG: in color picker, if you hit Done without saving your color picks, you 
are warned that you need to save. However if you cancel (in order to save) the color picker window closes.

Pre release Version 1.0 Dev 0.9.1 -- Dec 2011

Minor bug fixes and interface changes prior to release.

Since version 0.8.40:

New features:
Consistent menuing and can use Cmd-w to close windows.
Asks if you really want to quit when you use Cmd-q or Quit menu item.
Defaults button in table view restores all parameters (pie size etc) to defaults.
The last parameters you entered are kept between sessions (CPG quit and reopen).
File inputs for 0,1 or +/- data, with tab and comma separators all work.
You may have 3 or 4 header rows, the third being the one that labels the pie rows.

Bug fixes: 
Log removed (again) and Help revised to reflect a full release.

Since version 0.8.3:

New workflow for choosing colors: can intuitively add your own color swatch, 
save this in a file for reuse and remember the last color set used, or go back to defaults.

Since version 0.8.2:
 
About menu, and quit [Programmer: handled through FinderIntegration for Mac]
Preferences added (ditto).
Parameters set in various windows are remembered between sessions.
Location of windows remembered.

	
====================================
Contact: 
Please report bugs to:
imogenart@imogenart.co.uk
General comments to:
m.c.field@dundee.ac.uk
====================================