Usage

Menu Bar Items

Document

Command	Effect
New Document	Generates a new document. A document is the canvas onto which the plots, statistics, etc are drawn. Documents can be saved and printed.
Open Document	Opens a FCSalyzer document. This command does not open FACS data files. To open a data file, draw a plot into a document.
Save Document	Saves the currently selected document under its current name, overwriting the existing file with the same name. However, if the document was not opened from a file, a file dialog will appear to ask for a save name.
Save Document As	Saves the currently selected document after showing a file dialog to the user to enter a new name for the document.
Set Page Format	The Page Format defines the size of a single page of the document and the used page margins. This is also the page size used for printing. Changing the page size causes the document size to change as well, so that all objects (plots etc) still fit onto the document. Objects are not resized, when the page size changes!
Set Document Size	A document can consist of multiple pages, arranged in a grid. The maximum grid size is 10 x 10 pages.
Print Document	Brings up the printing dialog. FCSalyzer can't save documents as PDF files directly, but you can use a PDF-Printer like PDFCreator to print the documents into PDFs.
Export Document to PNG, data, statistics	Brings up an export dialog. There are a lot of possibilities: FCSalyzer can export the whole document as graphic to PNG and SVG. Also, the statistics shown in a document can be exported to a CSV file, as can be the event data shown in the document's plots. Especially interesting is the possiblity for batch processing and exporting: a list of FACS data files (FCS files) can be selected and the export cycles through each of the files.

Data Files

Command	Effect
View File Data	Brings up a dialog that lists all currently opened FCS data files with an option to inspect the data of the FCS files. This includes stored metadata such as parameter keywords, and also the event data values.
Format Datafiles	Brings up a dialog that lists all currently opened FCS data files with an option to change log transformation, compensation, parameter description and parameter multipliers of the FCS files.
Derive Parameters	Brings up a dialog that allows the definition of new parameters that are calculated based on existing parameters.
Attach Parameters	Brings up a dialog that allows to import and attach data as new parameters to FACS data files.
Edit Regions / Gates	Shows a dialog to rename regions and to create and rename gates.

Edit

Command	Effect
Copy	Copies the selected quadrant, region, or marker into the internal clipboard. No other object can currently be copied. The information is only stored in the internal clipboard of FCSalyzer and is not available to any other program. This is simply meant as an easy way to use quadrants and markers in many plots.
Paste	Pastes the content of the internal clipboard into the currently selected plot(s). Dot plots and density plots accept regions and quadrants, histogram plots accept markers. Existing quadrants will be replaced, existing markers remain.
Duplicate	Duplicates the selected object(s). Plots and comments are duplicated immediately, annotations and statistics only if they and their respective plots are selected. Quadrants and markers in the plots are also duplicated, but regions shown in the original plot are not shown in the duplicated plot.
Delete	Deletes the currently selected object(s), which may be plots, comments, statistics, annotations, quadrant, markers, or regions. If a region is deleted, gates using that region are invalidated.

Plot

Command	Effect
Format Plot/Overlay	Opens the dialog to format the plot and create overlays.
Export Plot/Overlay to PNG, data, statistics	Brings up an export dialog. There are a lot of possibilities: FCSalyzer can export the selected plot(s) as graphic to PNG and SVG. Also, their statistics can be exported to a CSV file, as can be the event data shown in the plots. Especially interesting is the possiblity for batch processing and exporting: a list of FACS data files (FCS files) can be selected and the export cycles through each of the files.
Set Datafile	Opens a file dialog to select a new data file for the selected plot(s).
Next Datafile	Opens the next data file in the directory of the data file(s) used for the selected plot(s). "Next" is defined by the order in which the files are presented to FCSalyzer by the operating system; FCSalyzer does not sort the files alphabetically or something like that.
Previous Datafile	Opens the previous data file in the directory of the data file(s) used for the selected plot(s). "Previous" is defined by the order in which the files are presented to FCSalyzer by the operating system; FCSalyzer does not sort the files alphabetically or something like that.
Step size ...	Brings up a dialog that allows to change the step size used for "Next" and "Previous Datafile". Step size 1 means the directly next/previous file in the directory, step size 2 means that one file is skipped, etc.
Manage color gradients	Brings up a dialog that allows to organize (create, modify, delete) color gradients that are used in density plots.
Annotate	Opens a dialog to select a FCS keyword whose value is then used as an annotation for the selected plot(s).
Statistics	Opens a dialog to select the statistics that are then shown for the selected plot(s).
Edit statistics	Allows to change the the properties of the currently selected statistics. These new properties become the standard for newly created statistics.
Edit markers	Shows a dialog to adjust the markers of the currently selected histogram. If more than one histogram is selected, the first found histogram is changed.

Arrangement

Command	Effect
Move ...	Moves the selected plots by a small increment. Please note that this option is meant for small adjustments of the plot positions. Keeping the arrow keys pressed down does not show smooth movement of the plots, but lets the plots jump around.
Align ...	Aligns the selected panels according to the respective out-most panel. So "Align Left" brings all selected panel to the left border to the left-most panel.

Help

Command	Effect
About	Shows a small dialog with the GPL3 license under which FCSalyzer is distributed.

Icon Bar

The icon bar contains buttons for drawing and adjusting objects in the document.

Icon	Effect
Selection	Sets the mouse to Selection-Mode. This allows to select objects on the document, move this objects, and change sizes and various properties. Selected objects are painted with a red border. If one of the selected objects are moved, all re moved. If the size of one object is changed, the size of all objects are set to the same size.
Quadrant	Allows to place a quadrant in dot plots and density plots.
Marker	Allows to place a marker in histogram plots.
Region	Allows to draw a region in dot plots and density plots.
Dot Plot	Allows to draw a dot plot onto the document. To draw, click and drag the selection border on the document. After releasing the mouse, a file dialog will appear to select the data file for the plot.
Density Plot	Allows to draw a density plot onto the document. To draw, click and drag the selection border on the document. After releasing the mouse, a file dialog will appear to select the data file for the plot.
Histogram	Allows to draw a histogram plot onto the document. To draw, click and drag the selection border on the document. After releasing the mouse, a file dialog will appear to select the data file for the plot.
Text Area	Allows to draw a comment onto the document. To draw, click and drag the selection border on the document. After releasing the mouse, an empty text area is created. To enter text, double-click on the area to enter edit mode. The text area's height is adjusted to the content size.
Font size	This drop-down box allows to change the font size of the currently selected objects.
Percentage	This drop-down box allows to change the percentages of the shown events in the the currently selected dot plots.
Gate	This drop-down box allows to change the gates of the currently selected plots.