Matrix2png - Revision history

Christoph: /* External links */

2012-07-11T20:19:10Z

‎External links

Christoph: /* Usage */

2012-07-11T19:24:47Z

‎Usage

Christoph at 02:35, 16 May 2012

2012-05-16T02:35:32Z

Christoph at 01:33, 24 July 2008

2008-07-24T01:33:38Z

Christoph: /* Documentation */

2008-06-24T00:59:24Z

‎Documentation

Christoph at 00:59, 24 June 2008

2008-06-24T00:59:01Z

Christoph at 07:08, 12 February 2007

2007-02-12T07:08:30Z

Christoph: /* Example */

2007-02-06T12:24:33Z

‎Example

Christoph at 11:56, 6 February 2007

2007-02-06T11:56:52Z

Christoph at 06:09, 14 October 2006

2006-10-14T06:09:20Z

New page

{{lowercase|title=matrix2png}}
'''matrix2png''' is a simple but powerful program for making visualizations of microarray data and many other data types. It generates [http://www.libpng.org/pub/png/ PNG] formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. It is useful for imaging all kinds of matrix-based data, not just microarray data. Matrix2png is open source.

== Reference ==
* Pavlidis P, Noble WS (2003). Matrix2png: A Utility for Visualizing Matrix Data. ''Bioinformatics, 19:295-296''.

== External links ==
* [http://microarray.cpmc.columbia.edu/matrix2png/ Official site]
* [http://microarray.cpmc.columbia.edu/pavlidis/lab/cgi-bin/matrix2png.cgi Web interface to matrix2png]
* [http://www.personal.psu.edu/cab38/ColorBrewer/ColorBrewer.html ColorBrewer] — colour schemes used in matrix2png

[[Category:Bioinformatics]]
[[Category:Graphics software]]

@@ Line 65: / Line 65: @@
 *[http://bioinformatics.ubc.ca/matrix2png/ Official site]
 *[http://bioinformatics.ubc.ca/pavlidis/lab/cgi-bin/matrix2png.cgi Web interface to matrix2png]
-*[http://www.personal.psu.edu/cab38/ColorBrewer/ColorBrewer.html ColorBrewer] &mdash; colour schemes used in matrix2png
+*[http://colorbrewer2.org/ ColorBrewer] &mdash; colour schemes used in matrix2png
 [[Category:Bioinformatics]]
 [[Category:Graphics software]]

@@ Line 5: / Line 5: @@
 ==Usage==
 ;<code>-data <file></code> : (required)
 ;<code>-desctext <file></code> : (optional)

@@ Line 2: / Line 2: @@
 '''matrix2png''' is a simple but powerful programme for making visualizations of microarray data and many other data types. It generates [http://www.libpng.org/pub/png/ PNG] formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. It is useful for imaging all kinds of matrix-based data, not just microarray data. Matrix2png is open source.
-The current version of matrix2png is '''1.0.6''' (April 2006).
+The current version of matrix2png is '''1.2.2''' (February 2012).
 ==Usage==

@@ Line 46: / Line 46: @@
 You can convert this to a PNG like so:
   {{prg_name|matrix2png}} -data foo.mat -size 18:18 -mincolor darkred -maxcolor white -c -r -s -con 1.0 >foo.png
 ==Documentation==

@@ Line 50: / Line 50: @@
 ;<code>-mincolor <value></code> : (ignored if using "<code>-map</code>"), <code>-maxcolor</code> (ignored if using "<code>-map</code>"), <code>-bkgcolor</code>: The colors which are used for the image scale. The smallest value in the image (or values less than or equal to the <code>minvalue</code>) are represented by <code>mincolor</code>, same idea for <code>maxcolor</code>. The background color is used for areas of the image not covered by the matrix data - which means that you may not see the background color at all. Colors can be selected by name or by <code>red:green:blue</code> triplets (values ranging from 0 to 255). Thus pure red is indicated by <code>255:0:0</code> while medium grey would be <code>128:128:128</code>. Colors which can be selected by name are:
 ::red, darkred, blue, darkblue, green, darkgreen, yellow, magenta, cyan, black, white, grey (or gray), orange, violet
-::Other colors are generated by interpolating between the min and max colors; by using color maps (below), you can use preset mappings that are more complex. (Defaults: <code>mincolor=blue; maxcolor=red; bkgcolor = white</code>.)
+::Other colors are generated by interpolating between the min and max colors; by using color maps (below), you can use preset mappings that are more complex. (Defaults: <code>mincolor=blue; maxcolor=red; bkgcolor=white</code>.)
 ==Reference==

@@ Line 1: / Line 1: @@
 {{lowercase|title=matrix2png}}
-'''matrix2png''' is a simple but powerful program for making visualizations of microarray data and many other data types. It generates [http://www.libpng.org/pub/png/ PNG] formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. It is useful for imaging all kinds of matrix-based data, not just microarray data. Matrix2png is open source.
+'''matrix2png''' is a simple but powerful programme for making visualizations of microarray data and many other data types. It generates [http://www.libpng.org/pub/png/ PNG] formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. It is useful for imaging all kinds of matrix-based data, not just microarray data. Matrix2png is open source.
 ==Usage==
- -data <file> (required)
+;<code>-data <file></code> : (required)
- -desctext <file>
+;<code>-desctext <file></code> : (optional)
- -range : values assigned to mincolor and maxcolor as min:max (default is data range)
+;<code>-range</code> : values assigned to mincolor and maxcolor as min:max (default is data range)
- -con : contrast (default = 1.0; applies only when not using -range option)
+;<code>-con</code> : contrast (default = 1.0; applies only when not using -range option)
- -size : pixel dimensions per value as x:y (default = 2:2)
+;<code>-size</code> : pixel dimensions per value as x:y (default = 2:2)
- -numcolors : number of colors (default = 64)
+;<code>-numcolors</code> : number of colours (default = 64)
- -minsize : minimum image size as x:y pixels
+;<code>-minsize</code> : minimum image size as x:y pixels
- -mincolor : color used at lowest value (name or r:g:b triplet) (default = blue)
+;<code>-mincolor</code> : colour used at lowest value (name or r:g:b triplet) (default = blue)
- -maxcolor : color used at highest value (name or r:g:b triplet) (default = red)
+;<code>-maxcolor</code> : colour used at highest value (name or r:g:b triplet) (default = red)
- -bkgcolor : color used as background (name or r:g:b triplet) (default = white)
+;<code>-bkgcolor</code> : colour used as background (name or r:g:b triplet) (default = white)
- -missingcolor : color used for missing values (name or r:g:b triplet) (default = grey)
+;<code>-missingcolor</code> : colour used for missing values (name or r:g:b triplet) (default = grey)
- -map : color choices from preset maps: overrides min/max colors and -b (default = 0 (none) )
+;<code>-map</code> : colour choices from preset maps: overrides min/max colours and -b (default = 0 (none))
- -discrete: Use discretized mapping of values to colors; use -dmap to assign a mapping file
+;<code>-discrete</code> : Use discretized mapping of values to colors; use -dmap to assign a mapping file
- -dmap <mapping file> : Discrete color mapping file to use for discrete mapping (default = preset)
+;<code>-dmap <mapping file></code> : Discrete colour mapping file to use for discrete mapping (default = preset)
- -numr : Number of rows to process starting from the top of the matrix by default
+;<code>-numr</code> : Number of rows to process starting from the top of the matrix by default
- -numc : Number of columns to process starting from the left edge of the matrix by default
+;<code>-numc</code> : Number of columns to process starting from the left edge of the matrix by default
- -startrow : Index of the first row to be processed; can combine with numr (default=1)
+;<code>-startrow</code> : Index of the first row to be processed; can combine with numr (default=1)
- -startcol : Index of the first column to be processed; can combine with numc (default=1)
+;<code>-startcol</code> : Index of the first column to be processed; can combine with numc (default=1)
- -trim : Trim this percent of data extremes when determining data range (only without the -range option)
+;<code>-trim</code> : Trim this percent of data extremes when determining data range (only without the -range option)
- -verbose : Verbosity of the output 1|2|3|4|5 (default=2)
+;<code>-verbose</code> : Verbosity of the output <code>1|2|3|4|5</code> (default=2)
- -title <title>: Add a title
+;<code>-title <title></code> : Add a title
- -z : Row-normalize the data to mean 0 and variance 1
+;<code>-z</code> : Row-normalize the data to mean 0 and variance 1
- -b : Middle of color range is black
+;<code>-b</code> : Middle of colour range is black
- -d : Add cell dividers
+;<code>-d</code> : Add cell dividers
- -s : Add scale bar
+;<code>-s</code> : Add scale bar
- -r : Add row names
+;<code>-r</code> : Add row names
- -c : Add column names
+;<code>-c</code> : Add column names
- -f : Data file has a format line
+;<code>-f</code> : Data file has a format line
- -e : Draw ellipses instead of rectangles
+;<code>-e</code> : Draw ellipses instead of rectangles
- -l : Log transform the data (base 2)
+;<code>-l</code> : Log transform the data (base 2)
 ===Example===
@@ Line 45: / Line 45: @@
   {{prg_name|matrix2png}} -data foo.mat -size 18:18 -mincolor darkred -maxcolor white -c -r -s -con 1.0 >foo.png
-== Reference ==
+==Reference==
-* Pavlidis P, Noble WS (2003). Matrix2png: A Utility for Visualizing Matrix Data. ''Bioinformatics, 19:295-296''.
+*Pavlidis P, Noble WS (2003). Matrix2png: A Utility for Visualizing Matrix Data. ''Bioinformatics, 19:295-296''.
-== External links ==
+==External links==
-* [http://microarray.cpmc.columbia.edu/matrix2png/ Official site]
+*[http://microarray.cpmc.columbia.edu/matrix2png/ Official site]
-* [http://microarray.cpmc.columbia.edu/pavlidis/lab/cgi-bin/matrix2png.cgi Web interface to matrix2png]
+*[http://microarray.cpmc.columbia.edu/pavlidis/lab/cgi-bin/matrix2png.cgi Web interface to matrix2png]
-* [http://www.personal.psu.edu/cab38/ColorBrewer/ColorBrewer.html ColorBrewer] &mdash; colour schemes used in matrix2png
+*[http://www.personal.psu.edu/cab38/ColorBrewer/ColorBrewer.html ColorBrewer] &mdash; colour schemes used in matrix2png
 [[Category:Bioinformatics]]
 [[Category:Graphics software]]