"All ASSAY data" – all channels that are members of the ASSAY class will be plotted.

"Displayed ASSAY data" – only displayed channels that are member of the ASSAY class will be plotted (this is the default setting).

"Select ASSAY channels from list" -- select ASSAY class channels from a two-panel selection list.

"All channels" – all numeric-type channels will be plotted. 

"All displayed channels" – all displayed numeric-type channels will be plotted.

Single Graph Size in mm. (default is 30 mm)

Optionally select a mask channel from the drop-down list. If specified, those non-dummy points in mask channel will be coloured red, while those dummy points in mask channel will be coloured light grey. If this value is left blank, or if "None" is selected, no masking is performed.

Channels selected for the drop-down list either have their CLASS attribute set to "MASK", or include the string "mask" in the channel name (case-insensitive).

Select a scaling option from the drop-down list to determine whether to scale the axes linearly or logarithmically. If "Default" is selected, the choice is made based on the "Log" attribute of each channel. The selections are made for the vertical, then horizontal channel (e.g. "Log-Lin" means a logarithmic vertical axis and a linear horizontal axis).

An optional title to be placed at the title box of the scatter plot. The default title is "Assay Scatter Plots".

Optional third channel to set the symbol colours from, using the input zone file. If this is left blank, the symbols are plotted red.

Select the colour scheme for rendering the symbol colours. If you mouse over the Colour table, a tooltip will display the name of the colour table file. To modify the selection, click on the colour entry and then navigate through the scheme categories.