Chapter 2. Feature Reference

Table of Contents

Command Line Options
Useful JVM Arguments
Main Program options
Dendrogram export options
Document Settings
Global Settings
Url Presets
Dendrogram Color Presets
Karyoscope Coordinates Presets
Url Settings
Dendrogram Font Settings
Dendrogram Pixel Settings
Karyoscope Coordinates Settings
Karyoscope Averaging Settings
Export of Selected Genes and Data to Tab-Delimited Text
Export of Dendrograms
Bounding Box
Java Treeview Modes
Informational Panels
Selection in Dendrogram
Url Linking in Dendrogram
Coloring Gene Names and Array Names
Creating a Scatterplot
Cursor hinting in Karyoscope
Zooming in Karyoscope
Selection Highlighting in Karyoscope
File Formats
Minimal File Requirements
Generalized CDT File
Coordinates Files for Karyoscope
Tree Files

Command Line Options

Useful JVM Arguments

The amount of memory can be specified using the standard arguments to the jvm, i.e. for 500 MB, use java -jar -Xmx500m TreeView.jar

Be aware that for windows, you may need to use javaw instead of java.

Main Program options

The main program options have a short and long form. An example command line to open a specified file using the "linked view" style would be java -Xmx500m -jar TreeView.jar -r

Main Program options

-r <file/url> (--resource=<file/url>)

File or url to load.

-t <type> (--type=<type>)

Open file with the specified type of viewer. Valid values are "linked" for multiple linked view (by default only dendrogram opens on new files), "kmeans" for k-means, "classic" for the classic, dendrogram only, and "auto" to autodetect (default)

-x <plugin> (--export=<plugin>

Export image from command line using the specified plugin instead of opening an interactive window. This argument requires that a resource to export is specified on the command line as well. Currently only the "Dendrogram" plugin is specified.

Dendrogram export options

When export to dendrogram is indicated using "-x Dendrogram", main program arguments can be terminated with "--" and additional dendrogram plugin arguments can be specified. An example complete command line would be:

java -jar TreeView.jar -r ./spellman.cdt -x Dendrogram -- -o /tmp/spellman.png -s 10x1 -a 0 -c 1

Dendrogram export options

-o <filename> (--output=<filename>)

(required) Filename to store image output in

-f <imageFormat> (--=<format>)

(optional) set output format, either 'png', 'gif' or 'ps' (defaults to extension of output file)

-s <widthxheight> (--scaling=<widthxheight>)

(optional) set pixel scaling as pixels for each array x pixels for each gene, or 1x10 for one pixel per array column and 10 pixels for each gene row, if you wanted to have gene names in the output

-a <headerIndexes> (--arrayHeaders=<headerIndexes>)

(optional) Comma separated list of array annotations to include in output. Example: -a 0 to include the first row of array annotations in the cdt file. By default no annotations are included.

-g <headerIndexes> (--geneHeaders=<headerIndexes>)

(optional) Comma separated list of gene annotations to include in output. Example: -g 0 to include the first column of array annotations in the cdt file. By default no annotations are included.

-h <pixels> (--atrHeight=<pixels>)

(optional) Explicitly set the height of the array tree.

-w <pixels> (--gtrWidth=<pixels>)

(optional) Explicitly set the width of the gene tree.

-b (--below)

(optional) boolean argument, moves the array annotations below the array tree

-c <value> (--contrast=<value>)

(optional) Explicitly set the contrast

-l <value> (--logcenter=<center>)

(optional) Take log base 2(data value/<center>) before applying the contrast. Useful if dealing with raw count data.

Note: Setting the contrast or logcenter values will modify the .jtv file and have a persistent effect when the file is reopened in java treeview

For operating systems which have a command line, a file or url can be specified. The following example demonstrates how to load the example off the website from the command line: java -jar TreeView.jar -r