This servlet can plot spot data for a bioassay or bioassay set. It uses
the JFreePlot package to generate the plots. It accepts the following parameters:
Plot parameters
Parameter |
Required |
Default value |
Description |
ID |
yes |
|
The SessionControl ID. See Application.getSessionControl(String, String) . |
bioassayset_id |
no |
|
The ID of the bioassay set to plot. If no value is specified the bioassay_id is
required. |
bioassay_id |
if a bioassay set hasn't been specified |
|
The ID of the bioassay to plot. |
type |
no |
scatter |
The type of plot to create. Supported values are "scatter", "histogram" or "cfplot". |
download |
no |
false |
A boolean value. If 1 or true, the browser will ask to save the image on the local disk. |
saveAs |
no |
|
If specified, the image is saved as a file in the BASE file structure. |
overwrite |
no |
false |
A boolean values, that is used with the "saveAs" parameter. If 1 or true, an
existing file will be overwritten with the image. |
width |
no |
600 |
The width of the generated image in pixels. Must be between 100 and 1000 pixels.
The default and max width can be configured in the web.xml file. |
height |
no |
400 |
The hieght of the generated image in pixels. Must be between 100 and 800.
The default and max height can be configured in the web.xml file. |
format |
no |
png |
The format of the image, "png" and "jpg" are the only supported values. |
xLog |
no |
false |
A boolean parameter. If 1 or true the logarithm of the x values is calculated
before plotting them. |
yLog |
no |
false |
A boolean parameter. If 1 or true the logarithm of the y values is calculated
before plotting them. |
x |
yes, unless type is "cfplot" |
|
The expression to plot on the x axis. Multiple x parameters may be specified
to plot multiple series. |
y |
no, unless type is "scatter" |
|
The expression to plot on the y axis. Multiple y parameters may be specified
to plot multiple series. |
filter |
no |
|
An optional filter expression that limits the result returned by the spot query. |
title |
no |
|
The title of the plot. If not specified the plot is generated without title. |
xLabel |
no |
|
The label on the x-axis. If not specified the plot is generated without label. |
yLabel |
no |
|
The label on the y-axis. If not specified the plot is generated without label. |
annotation |
no |
|
Can only be used when plotting a bioassay set. The only allowed value so far
is "bioassay" which plots the spots for each bioassay in different series and color. |
binSize |
no |
1.0 |
Only used for histogram plots. This is the range of values put into each
bin in the histogram. Ie. if the size is 1, the first bin may have values from -5 to -4,
the second bin from -4 to -3, and so on. |
yAggregate |
no |
count |
Only used for histogram plots. Determines what to plot on the y axis.
Allowed values are "count", "mean", "sum", "max", "min", "stdev". If a value other
than "count" is used an expression for the y-axis must also be specified. |
hiloAggregate |
no |
|
Only used for histogram plots when the yAggregate parameter isn't "count".
Allowed values are "hilomaxmin" and "hilostdev". This options adds a high-low bar
to each bin that is either the max/min range or the plotted value +/- 1 standard
deviation of the values in each bin.
|