Input File
The Expression data must be stored in a flat text file.
Each line should contain tab separated fields with floating point values.
At least one KEGG reaction ID or ENSG- or ENSGMUS-ID should be
present somewhere in each text line, to assign the line to a
certain KEGG reaction.
Other IDs and their mappings to KEGG reaction IDs might be
provided when a mapping is given.
The mapping file is specified with the command line option "-mapAffymetrixRid".
Columns that contain other data like gene description text is ignored.
The file is read by pressing the Enter key.
The data column header strings from the first line are shown in a list.
To check whether the data is correctly imported BUTTON:"list data" can be pressed in the debug panel.
The debug panel becomes visible by pressing BUTTON:"+".
Selecting a data column and display of the data in the Kegg Map
To select the current data column, the respective list element can be selected.
The column names are obtained from the first line of the file.
Scaling
The "Scale" panel contains a choice menu for a decimal factor and a slider.
Debugging
Expand the debug panel pressing BUTTON:"+".
A table with two columns becomes visible. The left column can
hold gene Id's such as ENSMUSG00000079681 ENSMUSG00000050810.
When a data column is selected in the list of data columns, the numeric data or NaN ( not a number) is written.
Cycling through data columns
To observe the difference between expression data columns, a convenient strategy is to select one
data column after the other and watch the blue bars on the reaction boxes in the Kegg maps.
This is easily done, if the data columns of interest are adjacent.
To cycle through non consecutive data columns, the grid of cells can be used.
The data columns of interest are typed into adjacent cells. For
example if the data columns "2", "5" and "8" need to be inspected,
then type "2" into the first cell of a row, "5" into the 2nd and "8"
into the 3ed.
By clicking into a cell, the respective data column is selected.
Navigation to other cells requires the cursor keys with or without ctrl, shift and alt.
Complex mathematical expressions
To see the sum of the data columns "2", "5" and "8" type "$2+$5+$8" into the cell.
Click JAVADOC:java.lang.Math for a complete list of mathematical functions in the Web browser.
Define color of the bars of boxes programmatically
Activating the check-box CB:"Compute color with own formula" a textfield appears where the user can enter an expression
that returns a color value. This option is only available for certain display modes.
Example:
value<5 ? YELLOW : Color.PINK
Click JAVADOC:java.awt.Color for a complete list of predefined colors.
Averaging
Often several lines in the datafile are assigned to one and the same RID. This is usually due to WIKI:Homology_(biology).
If CB:"Average" is deactivated, each line assigned to one RID results in one thin bar.
If CB:"Average" is activated, the values are averaged and displayed as border of different thicknes.