Table of Contents
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.
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 http://jtreeview.sourceforge.net/examples/DLim_color.cdt
Main Program options
File or url to load.
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)
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.
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
(required) Filename to store image output in
(optional) set output format, either 'png', 'gif' or 'ps' (defaults to extension of output file)
(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
(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.
(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.
(optional) Explicitly set the height of the array tree.
(optional) Explicitly set the width of the gene tree.
(optional) boolean argument, moves the array annotations below the array tree
(optional) Explicitly set the contrast
(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 http://jtreeview.sourceforge.net/examples/DLim_color.cdt